Variant rs7644410 details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.313 in 151,952 control chromosomes in the GnomAD database, including 7,744 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 0.31 ( 7744 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47589

AN:

151834

Hom.:

7741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.290

Gnomad AMR

AF:

0.316

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.323

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.313

AC:

47618

AN:

151952

Hom.:

7744

Cov.:

AF XY:

0.313

AC XY:

23257

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.243

Gnomad4 AMR

AF:

0.316

Gnomad4 ASJ

AF:

0.351

Gnomad4 EAS

AF:

0.416

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.353

Gnomad4 NFE

AF:

0.344

Gnomad4 OTH

AF:

0.328

Alfa

AF:

0.306

Hom.:

1051

Bravo

AF:

0.312

Asia WGS

AF:

0.346

AC:

1202

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

DANN

Benign

0.67

Splicing

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