dbSNP rs9332464: ANKDD1B:p.Ser169Asn (chr5-75625861-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001276713.2(ANKDD1B):c.506G>A(p.Ser169Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,535,122 control chromosomes in the GnomAD database, including 45,531 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 5619 hom., cov: 32)

Exomes 𝑓: 0.23 ( 39912 hom. )

Consequence

ANKDD1B
NM_001276713.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Variant links:

Genes affected

ANKDD1B (HGNC:32525): (ankyrin repeat and death domain containing 1B) Predicted to be involved in signal transduction. [provided by Alliance of Genome Resources, Apr 2022]

ANKDD1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0033620894).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKDD1B	NM_001276713.2 link	c.506G>A	p.Ser169Asn	missense_variant	Exon 5 of 14	ENST00000601380.4	NP_001263642.1	A6NHY2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKDD1B	ENST00000601380.4 link	c.506G>A	p.Ser169Asn	missense_variant	Exon 5 of 14	5	NM_001276713.2	ENSP00000471417.1		A6NHY2

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

40003

AN:

151918

Hom.:

5616

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.257

GnomAD3 exomes

AF:

0.258

AC:

35641

AN:

138322

Hom.:

5261

AF XY:

0.271

AC XY:

20268

AN XY:

74810

show subpopulations

Gnomad AFR exome

AF:

0.356

Gnomad AMR exome

AF:

0.155

Gnomad ASJ exome

AF:

0.276

Gnomad EAS exome

AF:

0.326

Gnomad SAS exome

AF:

0.422

Gnomad FIN exome

AF:

0.235

Gnomad NFE exome

AF:

0.212

Gnomad OTH exome

AF:

0.247

GnomAD4 exome

AF:

0.232

AC:

320399

AN:

1383086

Hom.:

39912

Cov.:

AF XY:

0.237

AC XY:

162090

AN XY:

682596

show subpopulations

Gnomad4 AFR exome

AF:

0.361

Gnomad4 AMR exome

AF:

0.162

Gnomad4 ASJ exome

AF:

0.277

Gnomad4 EAS exome

AF:

0.349

Gnomad4 SAS exome

AF:

0.421

Gnomad4 FIN exome

AF:

0.235

Gnomad4 NFE exome

AF:

0.210

Gnomad4 OTH exome

AF:

0.241

GnomAD4 genome

AF:

0.263

AC:

40030

AN:

152036

Hom.:

5619

Cov.:

AF XY:

0.267

AC XY:

19878

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.353

Gnomad4 AMR

AF:

0.201

Gnomad4 ASJ

AF:

0.276

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.431

Gnomad4 FIN

AF:

0.234

Gnomad4 NFE

AF:

0.210

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.240

Hom.:

1912

Bravo

AF:

0.260

TwinsUK

AF:

0.220

AC:

814

ALSPAC

AF:

0.212

AC:

817

ExAC

AF:

0.292

AC:

5630

Asia WGS

AF:

0.361

AC:

1252

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.053

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.75

CADD

Benign

2.3

DANN

Benign

0.26

DEOGEN2

Benign

0.0048

Eigen

Benign

-0.21

Eigen_PC

Benign

-0.17

FATHMM_MKL

Benign

0.010

LIST_S2

Benign

0.25

MetaRNN

Benign

0.0034

MutationAssessor

Benign

1.3

PrimateAI

Benign

0.43

Sift4G

Benign

0.80

Vest4

0.045

ClinPred

0.0023

GERP RS

3.6

Varity_R

0.036

gMVP

0.34

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over