Variant chr5-75653218-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001276713.2(ANKDD1B):c.875T>C(p.Val292Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00825 in 1,535,996 control chromosomes in the GnomAD database, including 687 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.039 ( 348 hom., cov: 33)

Exomes 𝑓: 0.0049 ( 339 hom. )

Consequence

ANKDD1B
NM_001276713.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.662

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0014633238).

BP6

Variant 5-75653218-T-C is Benign according to our data. Variant chr5-75653218-T-C is described in ClinVar as [Benign]. Clinvar id is 792001.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKDD1B	NM_001276713.2 linkuse as main transcript	c.875T>C	p.Val292Ala	missense_variant	8/14	ENST00000601380.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKDD1B	ENST00000601380.4 linkuse as main transcript	c.875T>C	p.Val292Ala	missense_variant	8/14	5	NM_001276713.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0391

AC:

5957

AN:

152162

Hom.:

350

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0220

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0281

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000735

Gnomad OTH

AF:

0.0340

GnomAD3 exomes

AF:

0.0112

AC:

1532

AN:

137058

Hom.:

AF XY:

0.00900

AC XY:

671

AN XY:

74524

show subpopulations

Gnomad AFR exome

AF:

0.134

Gnomad AMR exome

AF:

0.0101

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0287

Gnomad SAS exome

AF:

0.000934

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00108

Gnomad OTH exome

AF:

0.00929

GnomAD4 exome

AF:

0.00486

AC:

6724

AN:

1383716

Hom.:

339

Cov.:

AF XY:

0.00438

AC XY:

2992

AN XY:

682796

show subpopulations

Gnomad4 AFR exome

AF:

0.135

Gnomad4 AMR exome

AF:

0.0117

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0198

Gnomad4 SAS exome

AF:

0.00103

Gnomad4 FIN exome

AF:

0.0000295

Gnomad4 NFE exome

AF:

0.000455

Gnomad4 OTH exome

AF:

0.0122

GnomAD4 genome

AF:

0.0391

AC:

5954

AN:

152280

Hom.:

348

Cov.:

AF XY:

0.0369

AC XY:

2745

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.0220

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0282

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000735

Gnomad4 OTH

AF:

0.0336

Alfa

AF:

0.0166

Hom.:

Bravo

AF:

0.0453

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000519

AC:

ExAC

AF:

0.00726

AC:

136

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.71

CADD

Benign

2.2

DANN

Benign

0.60

DEOGEN2

Benign

0.00097

FATHMM_MKL

Benign

0.088

LIST_S2

Benign

0.36

MetaRNN

Benign

0.0015

MutationAssessor

Benign

-0.23

PrimateAI

Benign

0.30

Sift4G

Benign

0.58

Vest4

0.067

GERP RS

2.9

Varity_R

0.028

gMVP

0.33

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over