rs963274

Positions:

• chr6-50406398-G-T

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 0.102 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0813 Hom.: 138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs963274; hg19: chr6-50374111;