rs950286

Variant names:

• chr6-429457-G-A
• rs950286

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 0.144 in 152,186 control chromosomes in the GnomAD database, including 1,810 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 0.14 (1810 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 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: 0.144 AC: 21829 AN: 152068 Hom.: 1806 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.144 AC: 21863 AN: 152186 Hom.: 1810 Cov.: 33 AF XY: 0.145 AC XY: 10776 AN XY: 74402

African (AFR) AF: 0.216 AC: 8944 AN: 41490

American (AMR) AF: 0.130 AC: 1992 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1272 AN: 5184

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4828

European-Finnish (FIN) AF: 0.162 AC: 1717 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6996 AN: 68006

Other (OTH) AF: 0.132 AC: 279 AN: 2114

Alfa AF: 0.117 Hom.: 2936

Bravo AF: 0.147

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.26
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs950286; hg19: chr6-429457;