Genetic Variant ENST00000518253.5:n.2012G>A (chr6-89631015-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000518253.5(ANKRD6):n.2012G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,492,234 control chromosomes in the GnomAD database, including 23,351 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2369 hom., cov: 33)

Exomes 𝑓: 0.18 ( 20982 hom. )

Consequence

ANKRD6
ENST00000518253.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.297

Publications

9 publications found

Variant links:

Genes affected

ANKRD6 (HGNC:17280): (ankyrin repeat domain 6) Predicted to be involved in negative regulation of canonical Wnt signaling pathway and positive regulation of JNK cascade. Predicted to act upstream of or within positive regulation of Wnt signaling pathway, planar cell polarity pathway. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD6 links:

LYRM2 (HGNC:25229): (LYR motif containing 2)

LYRM2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD6	NM_001242809.2 link	c.*11G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000339746.9	NP_001229738.1	Q9Y2G4-2B7Z3D2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD6	ENST00000339746.9 link	c.*11G>A		3_prime_UTR_variant	Exon 16 of 16	1	NM_001242809.2	ENSP00000345767.4		Q9Y2G4-2

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26476

AN:

152050

Hom.:

2367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.219

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.177

Gnomad OTH

AF:

0.185

GnomAD2 exomes

AF:

0.176

AC:

19092

AN:

108432

AF XY:

0.175

show subpopulations

Gnomad AFR exome

AF:

0.182

Gnomad AMR exome

AF:

0.144

Gnomad ASJ exome

AF:

0.223

Gnomad EAS exome

AF:

0.214

Gnomad FIN exome

AF:

0.185

Gnomad NFE exome

AF:

0.190

Gnomad OTH exome

AF:

0.172

GnomAD4 exome

AF:

0.175

AC:

234751

AN:

1340066

Hom.:

20982

Cov.:

AF XY:

0.174

AC XY:

114388

AN XY:

656506

show subpopulations

African (AFR)

AF:

0.170

AC:

4946

AN:

29090

American (AMR)

AF:

0.137

AC:

3226

AN:

23542

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

4568

AN:

21484

East Asian (EAS)

AF:

0.194

AC:

6923

AN:

35738

South Asian (SAS)

AF:

0.109

AC:

7533

AN:

69286

European-Finnish (FIN)

AF:

0.173

AC:

7509

AN:

43476

Middle Eastern (MID)

AF:

0.132

AC:

717

AN:

5412

European-Non Finnish (NFE)

AF:

0.179

AC:

189309

AN:

1056440

Other (OTH)

AF:

0.180

AC:

10020

AN:

55598

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

10044

20088

30132

40176

50220

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6884

13768

20652

27536

34420

<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:

0.174

AC:

26488

AN:

152168

Hom.:

2369

Cov.:

AF XY:

0.175

AC XY:

13033

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.171

AC:

7083

AN:

41516

American (AMR)

AF:

0.165

AC:

2524

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

725

AN:

3470

East Asian (EAS)

AF:

0.218

AC:

1131

AN:

5184

South Asian (SAS)

AF:

0.113

AC:

544

AN:

4822

European-Finnish (FIN)

AF:

0.182

AC:

1925

AN:

10580

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.177

AC:

12060

AN:

67996

Other (OTH)

AF:

0.182

AC:

382

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1125

2251

3376

4502

5627

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.175

Hom.:

674

Bravo

AF:

0.173

Asia WGS

AF:

0.156

AC:

544

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.60

(source)

DANN

Benign

0.49

PhyloP100

-0.30

Mutation Taster

=100/0

polymorphism (auto)

(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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over