chr4-7157975-G-A

Variant names:

• chr4-7157975-G-A
• rs3894944

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.782 in 152,150 control chromosomes in the GnomAD database, including 46,541 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 0.78 (46541 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118873 AN: 152032 Hom.: 46497 Cov.: 33

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.782 AC: 118976 AN: 152150 Hom.: 46541 Cov.: 33 AF XY: 0.786 AC XY: 58485 AN XY: 74370

African (AFR) AF: 0.760 AC: 31547 AN: 41482

American (AMR) AF: 0.826 AC: 12625 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2435 AN: 3470

East Asian (EAS) AF: 0.852 AC: 4412 AN: 5180

South Asian (SAS) AF: 0.765 AC: 3683 AN: 4816

European-Finnish (FIN) AF: 0.845 AC: 8949 AN: 10586

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52739 AN: 68020

Other (OTH) AF: 0.784 AC: 1652 AN: 2108

Alfa AF: 0.784 Hom.: 7541

Bravo AF: 0.781

Asia WGS AF: 0.784 AC: 2730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.12
PhyloP100		-2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3894944; hg19: chr4-7159702;