rs9491646

Variant names:

• chr6-98479487-G-A
• rs9491646

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 0.0491 in 151,950 control chromosomes in the GnomAD database, including 229 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 (229 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0719 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: 0.0491 AC: 7451 AN: 151832 Hom.: 228 Cov.: 32

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.00756

Gnomad SAS AF: 0.00828

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0491 AC: 7462 AN: 151950 Hom.: 229 Cov.: 32 AF XY: 0.0507 AC XY: 3766 AN XY: 74262

Gnomad4 AFR AF: 0.0741

Gnomad4 AMR AF: 0.0623

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.00738

Gnomad4 SAS AF: 0.00808

Gnomad4 FIN AF: 0.0633

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0379 Hom.: 157

Bravo AF: 0.0506

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9491646; hg19: chr6-98927363;