Genetic Variant ANKRD36:c.-4G>C (chr2-97113736-G-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001354587.1(ANKRD36):c.-4G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00125 in 1,608,458 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0011 ( 25 hom. )

Consequence

ANKRD36
NM_001354587.1 5_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0200

Publications

0 publications found

Variant links:

Genes affected

ANKRD36 (HGNC:24079): (ankyrin repeat domain 36)

ANKRD36 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 2-97113736-G-C is Benign according to our data. Variant chr2-97113736-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2651154.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001354587.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD36	NM_001354587.1	MANE Select	c.-4G>C		5_prime_UTR	Exon 1 of 76	NP_001341516.1	A6QL64-1
	ANKRD36	NM_198555.4		c.-4G>C		5_prime_UTR	Exon 1 of 3	NP_940957.3	A6QL64-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ANKRD36	ENST00000420699.9	TSL:5 MANE Select	c.-4G>C	5_prime_UTR	Exon 1 of 76	ENSP00000391950.4	A6QL64-1
ANKRD36	ENST00000452478.2	TSL:1	n.185G>C	non_coding_transcript_exon	Exon 1 of 3
ANKRD36	ENST00000461153.7	TSL:5	c.-4G>C	5_prime_UTR	Exon 1 of 75	ENSP00000419530.3	A6QL64-1

Frequencies

GnomAD3 genomes

AF:

0.00224

AC:

336

AN:

150278

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000556

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00304

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000199

Gnomad SAS

AF:

0.00105

Gnomad FIN

AF:

0.000914

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00352

Gnomad OTH

AF:

0.00433

GnomAD2 exomes

AF:

0.000637

AC:

157

AN:

246496

AF XY:

0.000596

show subpopulations

Gnomad AFR exome

AF:

0.0000651

Gnomad AMR exome

AF:

0.000967

Gnomad ASJ exome

AF:

0.0000999

Gnomad EAS exome

AF:

0.000113

Gnomad FIN exome

AF:

0.000142

Gnomad NFE exome

AF:

0.000966

Gnomad OTH exome

AF:

0.000669

GnomAD4 exome

AF:

0.00115

AC:

1673

AN:

1458080

Hom.:

Cov.:

AF XY:

0.00121

AC XY:

874

AN XY:

725296

show subpopulations

African (AFR)

AF:

0.000120

AC:

AN:

33470

American (AMR)

AF:

0.00162

AC:

AN:

44462

Ashkenazi Jewish (ASJ)

AF:

0.000153

AC:

AN:

26104

East Asian (EAS)

AF:

0.0000767

AC:

AN:

39118

South Asian (SAS)

AF:

0.000628

AC:

AN:

86052

European-Finnish (FIN)

AF:

0.000680

AC:

AN:

52910

Middle Eastern (MID)

AF:

0.00696

AC:

AN:

5744

European-Non Finnish (NFE)

AF:

0.00120

AC:

1333

AN:

1110036

Other (OTH)

AF:

0.00211

AC:

127

AN:

60184

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.421

Heterozygous variant carriers

186

280

373

466

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00223

AC:

336

AN:

150378

Hom.:

Cov.:

AF XY:

0.00209

AC XY:

153

AN XY:

73268

show subpopulations

African (AFR)

AF:

0.000554

AC:

AN:

41516

American (AMR)

AF:

0.00303

AC:

AN:

15172

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3462

East Asian (EAS)

AF:

0.000200

AC:

AN:

5012

South Asian (SAS)

AF:

0.00105

AC:

AN:

4758

European-Finnish (FIN)

AF:

0.000914

AC:

AN:

9846

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00352

AC:

237

AN:

67330

Other (OTH)

AF:

0.00432

AC:

AN:

2082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.441

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00113

Hom.:

Bravo

AF:

0.00264

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.7

(source)

DANN

Benign

0.50

PhyloP100

-0.020

PromoterAI

0.20

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=300/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over