rs6957902

Variant names:

• chr7-69473632-C-T
• rs6957902

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 0.379 in 151,974 control chromosomes in the GnomAD database, including 11,251 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 0.38 (11251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 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: 0.379 AC: 57518 AN: 151856 Hom.: 11226 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.379 AC: 57587 AN: 151974 Hom.: 11251 Cov.: 32 AF XY: 0.381 AC XY: 28328 AN XY: 74288

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.381

Alfa AF: 0.345 Hom.: 4142

Bravo AF: 0.385

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6957902; hg19: chr7-68938618;