rs6954895

Variant names:

• chr7-35546596-T-C
• rs6954895

Variant summary

Our verdict is Benign. Variant got -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

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 (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.0783

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.305

Alfa AF: 0.268 Hom.: 10012

Bravo AF: 0.285

Asia WGS AF: 0.242 AC: 842 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	5.5
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6954895; hg19: chr7-35586206;