rs6953983

Variant names:

• chr7-96778461-A-G
• rs6953983

Your query was ambiguous. Multiple possible variants found:

• chr7-96778461-A-G
• chr7-96778461-A-T

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 0.535 in 152,046 control chromosomes in the GnomAD database, including 24,656 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 0.53 (24656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81330 AN: 151928 Hom.: 24671 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.535 AC: 81326 AN: 152046 Hom.: 24656 Cov.: 32 AF XY: 0.533 AC XY: 39618 AN XY: 74332

African (AFR) AF: 0.236 AC: 9782 AN: 41500

American (AMR) AF: 0.512 AC: 7818 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3888 AN: 5164

South Asian (SAS) AF: 0.607 AC: 2927 AN: 4826

European-Finnish (FIN) AF: 0.610 AC: 6427 AN: 10540

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46173 AN: 67970

Other (OTH) AF: 0.566 AC: 1194 AN: 2108

Alfa AF: 0.634 Hom.: 92367

Bravo AF: 0.517

Asia WGS AF: 0.602 AC: 2095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.67
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs6953983; hg19: chr7-96407773;