rs6951646

chr7-21139308-G-A

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 0.133 in 152,168 control chromosomes in the GnomAD database, including 1,973 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 0.13 (1973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20135 AN: 152050 Hom.: 1965 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.133 AC: 20166 AN: 152168 Hom.: 1973 Cov.: 32 AF XY: 0.128 AC XY: 9509 AN XY: 74388

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.0872

Gnomad4 ASJ AF: 0.0901

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.0415

Gnomad4 NFE AF: 0.0817

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0895 Hom.: 362

Bravo AF: 0.142

Asia WGS AF: 0.101 AC: 350 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	1.3
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6951646; hg19: chr7-21178927; COSMIC: COSV70887030;