rs220966

Variant names:

• chr6-94265967-C-T
• rs220966

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 0.103 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.152 AC: 6293 AN: 41452

American (AMR) AF: 0.0884 AC: 1349 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5162

South Asian (SAS) AF: 0.0915 AC: 439 AN: 4800

European-Finnish (FIN) AF: 0.0683 AC: 722 AN: 10578

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0889 AC: 6043 AN: 67992

Other (OTH) AF: 0.108 AC: 228 AN: 2108

Alfa AF: 0.0965 Hom.: 109

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

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