rs220966

Positions:

• chr6-94265967-C-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 0.103 in 152,028 control chromosomes in the GnomAD database, including 876 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 (876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15593 AN: 151910 Hom.: 872 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.103 AC: 15609 AN: 152028 Hom.: 876 Cov.: 32 AF XY: 0.101 AC XY: 7511 AN XY: 74302

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0884

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0915

Gnomad4 FIN AF: 0.0683

Gnomad4 NFE AF: 0.0889

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0945 Hom.: 102

Bravo AF: 0.104

Asia WGS AF: 0.0590 AC: 207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs220966; hg19: chr6-94975685; COSMIC: COSV69413874;