Genetic Variant ANKRD36:c.2173-3A>C (chr2-97189215-A-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001354587.1(ANKRD36):c.2173-3A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 44 hom., cov: 15)

Exomes 𝑓: 0.0012 ( 305 hom. )

Consequence

ANKRD36
NM_001354587.1 splice_region, intron

Scores

Splicing: ADA: 0.00004899

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.321

Variant links:

Genes affected

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

ANKRD36 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BP6

Variant 2-97189215-A-C is Benign according to our data. Variant chr2-97189215-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2651163.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00119 (792/666302) while in subpopulation MID AF= 0.0243 (81/3334). AF 95% confidence interval is 0.02. There are 305 homozygotes in gnomad4_exome. There are 436 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1 link	c.2173-3A>C		splice_region_variant, intron_variant	Intron 33 of 75	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ANKRD36	ENST00000420699.9 link	c.2173-3A>C	splice_region_variant, intron_variant	Intron 33 of 75	5	NM_001354587.1	ENSP00000391950.4	A6QL64-1
ANKRD36	ENST00000461153.7 link	c.2173-3A>C	splice_region_variant, intron_variant	Intron 33 of 74	5		ENSP00000419530.3	A6QL64-1
ANKRD36	ENST00000652721.1 link	c.2173-3A>C	splice_region_variant, intron_variant	Intron 33 of 75			ENSP00000498611.1	A6QL64-1

Frequencies

GnomAD3 genomes

AF:

0.00132

AC:

117

AN:

88876

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000313

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00363

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000884

Gnomad SAS

AF:

0.000505

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00202

Gnomad OTH

AF:

0.00396

GnomAD3 exomes

AF:

0.000771

AC:

103

AN:

133530

Hom.:

AF XY:

0.000738

AC XY:

AN XY:

71834

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00113

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000546

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00145

Gnomad OTH exome

AF:

0.00162

GnomAD4 exome

AF:

0.00119

AC:

792

AN:

666302

Hom.:

305

Cov.:

AF XY:

0.00129

AC XY:

436

AN XY:

338688

show subpopulations

Gnomad4 AFR exome

AF:

0.000504

Gnomad4 AMR exome

AF:

0.00151

Gnomad4 ASJ exome

AF:

0.0000614

Gnomad4 EAS exome

AF:

0.0000277

Gnomad4 SAS exome

AF:

0.000378

Gnomad4 FIN exome

AF:

0.000125

Gnomad4 NFE exome

AF:

0.00131

Gnomad4 OTH exome

AF:

0.00184

GnomAD4 genome

AF:

0.00131

AC:

117

AN:

89008

Hom.:

Cov.:

AF XY:

0.00149

AC XY:

AN XY:

43538

show subpopulations

Gnomad4 AFR

AF:

0.000312

Gnomad4 AMR

AF:

0.00362

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000887

Gnomad4 SAS

AF:

0.000505

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00202

Gnomad4 OTH

AF:

0.00390

Alfa

AF:

0.00101

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ANKRD36: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.93

DANN

Benign

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000049

dbscSNV1_RF

Benign

0.020

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over