rs10491303

Variant names:

• chr5-136890859-A-G
• rs10491303

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.025 in 152,300 control chromosomes in the GnomAD database, including 98 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 0.025 (98 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.025 (3802/152300) while in subpopulation AFR AF = 0.0508 (2112/41568). AF 95% confidence interval is 0.049. There are 98 homozygotes in GnomAd4. There are 1833 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 98 gene

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: 0.0250 AC: 3799 AN: 152182 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0177

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.00875

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0250 AC: 3802 AN: 152300 Hom.: 98 Cov.: 32 AF XY: 0.0246 AC XY: 1833 AN XY: 74484

African (AFR) AF: 0.0508 AC: 2112 AN: 41568

American (AMR) AF: 0.0176 AC: 270 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3470

East Asian (EAS) AF: 0.0265 AC: 137 AN: 5176

South Asian (SAS) AF: 0.0358 AC: 173 AN: 4830

European-Finnish (FIN) AF: 0.00875 AC: 93 AN: 10624

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0131 AC: 890 AN: 68024

Other (OTH) AF: 0.0228 AC: 48 AN: 2104

Alfa AF: 0.0194 Hom.: 23

Bravo AF: 0.0265

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs10491303; hg19: chr5-136226548;