rs9381477

Variant names:

• chr6-46739843-G-A
• rs9381477

Your query was ambiguous. Multiple possible variants found:

• chr6-46739843-G-A
• chr6-46739843-G-C

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 0.204 in 152,032 control chromosomes in the GnomAD database, including 3,536 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 0.20 (3536 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 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: 0.204 AC: 30963 AN: 151914 Hom.: 3527 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.204 AC: 30993 AN: 152032 Hom.: 3536 Cov.: 32 AF XY: 0.211 AC XY: 15701 AN XY: 74334

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.220

Alfa AF: 0.213 Hom.: 620

Bravo AF: 0.195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9381477; hg19: chr6-46707580;