rs9491640

Variant names:

• chr6-98471388-C-A
• rs9491640

Your query was ambiguous. Multiple possible variants found:

• chr6-98471388-C-A
• chr6-98471388-C-G

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 0.0492 in 151,960 control chromosomes in the GnomAD database, including 230 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 0.049 (230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0722 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: 0.0492 AC: 7470 AN: 151842 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0743

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0625

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.00775

Gnomad SAS AF: 0.00831

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0492 AC: 7481 AN: 151960 Hom.: 230 Cov.: 32 AF XY: 0.0509 AC XY: 3776 AN XY: 74230

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.0624

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.00757

Gnomad4 SAS AF: 0.00811

Gnomad4 FIN AF: 0.0637

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.0442

Alfa AF: 0.0341 Hom.: 149

Bravo AF: 0.0506

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9491640; hg19: chr6-98919264;