rs10491604

Variant names:

• chr9-86733652-G-A
• rs10491604

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 0.0376 in 152,258 control chromosomes in the GnomAD database, including 270 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 0.038 (270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.14 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: 0.0375 AC: 5706 AN: 152140 Hom.: 265 Cov.: 32

Gnomad AFR AF: 0.0122

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0263

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.0784

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0376 AC: 5728 AN: 152258 Hom.: 270 Cov.: 32 AF XY: 0.0389 AC XY: 2896 AN XY: 74452

African (AFR) AF: 0.0122 AC: 507 AN: 41560

American (AMR) AF: 0.145 AC: 2211 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0263 AC: 91 AN: 3464

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5174

South Asian (SAS) AF: 0.0789 AC: 381 AN: 4828

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10622

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0320 AC: 2174 AN: 68012

Other (OTH) AF: 0.0562 AC: 119 AN: 2116

Alfa AF: 0.0356 Hom.: 79

Bravo AF: 0.0463

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs10491604; hg19: chr9-89348567;