rs963274

Variant names:

• chr6-50406398-G-T
• rs963274

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 0.102 in 152,032 control chromosomes in the GnomAD database, including 1,170 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 0.10 (1170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.102 AC: 15553 AN: 151912 Hom.: 1169 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.102 AC: 15570 AN: 152032 Hom.: 1170 Cov.: 32 AF XY: 0.0983 AC XY: 7308 AN XY: 74346

African (AFR) AF: 0.202 AC: 8388 AN: 41432

American (AMR) AF: 0.0889 AC: 1357 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3464

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4818

European-Finnish (FIN) AF: 0.0308 AC: 326 AN: 10584

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0689 AC: 4683 AN: 67978

Other (OTH) AF: 0.112 AC: 238 AN: 2116

Alfa AF: 0.0839 Hom.: 147

Bravo AF: 0.113

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.024
DANN	Benign	0.51
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs963274; hg19: chr6-50374111;