rs9491385

Variant names:

• chr6-125311885-T-C
• rs9491385

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 0.526 in 151,950 control chromosomes in the GnomAD database, including 22,694 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 0.53 (22694 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 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: 0.526 AC: 79893 AN: 151832 Hom.: 22651 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.526 AC: 79998 AN: 151950 Hom.: 22694 Cov.: 31 AF XY: 0.520 AC XY: 38622 AN XY: 74274

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.520

Alfa AF: 0.481 Hom.: 4593

Bravo AF: 0.543

Asia WGS AF: 0.493 AC: 1715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9491385; hg19: chr6-125633031;