rs9405313

Variant names:

• chr6-6667948-C-A
• rs9405313

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 0.143 in 152,222 control chromosomes in the GnomAD database, including 1,631 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 (1631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.222 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: 0.143 AC: 21693 AN: 152104 Hom.: 1625 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.143 AC: 21726 AN: 152222 Hom.: 1631 Cov.: 32 AF XY: 0.144 AC XY: 10691 AN XY: 74420

African (AFR) AF: 0.151 AC: 6292 AN: 41534

American (AMR) AF: 0.154 AC: 2351 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1120 AN: 5170

South Asian (SAS) AF: 0.233 AC: 1125 AN: 4830

European-Finnish (FIN) AF: 0.0926 AC: 982 AN: 10608

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8899 AN: 68002

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.138 Hom.: 2694

Bravo AF: 0.147

Asia WGS AF: 0.193 AC: 672 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	6.2
DANN	Benign	0.80
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9405313; hg19: chr6-6668181;