rs6954895

Variant names:

• chr7-35546596-T-C
• rs6954895

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 0.275 in 152,090 control chromosomes in the GnomAD database, including 6,171 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 0.27 (6171 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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: 0.275 AC: 41779 AN: 151972 Hom.: 6173 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.0777

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.275 AC: 41793 AN: 152090 Hom.: 6171 Cov.: 32 AF XY: 0.270 AC XY: 20105 AN XY: 74366

African (AFR) AF: 0.360 AC: 14916 AN: 41454

American (AMR) AF: 0.240 AC: 3678 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3466

East Asian (EAS) AF: 0.0783 AC: 406 AN: 5188

South Asian (SAS) AF: 0.358 AC: 1724 AN: 4814

European-Finnish (FIN) AF: 0.151 AC: 1601 AN: 10584

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17233 AN: 67974

Other (OTH) AF: 0.305 AC: 643 AN: 2110

Alfa AF: 0.266 Hom.: 22835

Bravo AF: 0.285

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.37
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6954895; hg19: chr7-35586206;