rs9491385

Variant names:

• chr6-125311885-T-C
• rs9491385

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 0.526 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.760 AC: 31518 AN: 41446

American (AMR) AF: 0.447 AC: 6823 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1689 AN: 3468

East Asian (EAS) AF: 0.422 AC: 2178 AN: 5162

South Asian (SAS) AF: 0.502 AC: 2409 AN: 4800

European-Finnish (FIN) AF: 0.347 AC: 3661 AN: 10552

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30170 AN: 67954

Other (OTH) AF: 0.520 AC: 1098 AN: 2112

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9491385; hg19: chr6-125633031;