Variant 7-118224974-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_019644.4(ANKRD7):c.144G>T(p.Lys48Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,614,074 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 0.0088 ( 20 hom., cov: 31)

Exomes 𝑓: 0.00091 ( 26 hom. )

Consequence

ANKRD7
NM_019644.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38

Variant links:

Genes affected

ANKRD7 (HGNC:18588): (ankyrin repeat domain 7) Predicted to act upstream of or within blastocyst hatching. Located in centrosome and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD7 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=0.0057581663).

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00885 (1347/152280) while in subpopulation AFR AF= 0.0314 (1306/41558). AF 95% confidence interval is 0.03. There are 20 homozygotes in gnomad4. There are 651 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD7	NM_019644.4 link	c.144G>T	p.Lys48Asn	missense_variant	1/7	ENST00000265224.9	NP_062618.2	Q92527-1A0A140VJE5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD7	ENST00000265224.9 link	c.144G>T	p.Lys48Asn	missense_variant	1/7	1	NM_019644.4	ENSP00000265224.4		Q92527-1

Frequencies

GnomAD3 genomes

AF:

0.00878

AC:

1336

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0313

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000103

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00239

AC:

590

AN:

247188

Hom.:

AF XY:

0.00183

AC XY:

246

AN XY:

134354

show subpopulations

Gnomad AFR exome

AF:

0.0357

Gnomad AMR exome

AF:

0.000667

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000540

Gnomad OTH exome

AF:

0.00149

GnomAD4 exome

AF:

0.000913

AC:

1334

AN:

1461794

Hom.:

Cov.:

AF XY:

0.000771

AC XY:

561

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.0339

Gnomad4 AMR exome

AF:

0.000917

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000464

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000324

Gnomad4 OTH exome

AF:

0.00176

GnomAD4 genome

AF:

0.00885

AC:

1347

AN:

152280

Hom.:

Cov.:

AF XY:

0.00874

AC XY:

651

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0314

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000103

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00457

Hom.:

Bravo

AF:

0.0106

ESP6500AA

AF:

0.0314

AC:

116

ESP6500EA

AF:

0.000122

AC:

ExAC

AF:

0.00305

AC:

369

EpiCase

AF:

0.000164

EpiControl

AF:

0.0000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.43

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.039

T;.;.

Eigen

Benign

-0.41

Eigen_PC

Benign

-0.56

FATHMM_MKL

Benign

0.43

LIST_S2

Benign

0.60

T;T;T

MetaRNN

Benign

0.0058

T;T;T

MetaSVM

Benign

-0.88

MutationAssessor

Benign

0.23

N;.;.

PrimateAI

Benign

0.44

PROVEAN

Benign

-2.3

N;N;.

REVEL

Benign

0.16

Sift

Uncertain

0.028

D;T;.

Sift4G

Benign

0.30

T;T;T

Polyphen

1.0

D;.;.

Vest4

0.20

MutPred

0.44

Loss of MoRF binding (P = 0.053);Loss of MoRF binding (P = 0.053);Loss of MoRF binding (P = 0.053);

MVP

0.74

MPC

1.0

ClinPred

0.040

GERP RS

0.28

Varity_R

0.12

gMVP

0.11

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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