rs10491302

Variant names:

• chr5-136965783-G-A
• rs10491302

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 0.0211 in 152,206 control chromosomes in the GnomAD database, including 92 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 0.021 (92 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0211 (3210/152206) while in subpopulation AFR AF = 0.0506 (2100/41524). AF 95% confidence interval is 0.0488. There are 92 homozygotes in GnomAd4. There are 1576 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 92 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: 0.0210 AC: 3201 AN: 152088 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.0505

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0128

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00634

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0211 AC: 3210 AN: 152206 Hom.: 92 Cov.: 32 AF XY: 0.0212 AC XY: 1576 AN XY: 74422

African (AFR) AF: 0.0506 AC: 2100 AN: 41524

American (AMR) AF: 0.0128 AC: 195 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5168

South Asian (SAS) AF: 0.0398 AC: 192 AN: 4824

European-Finnish (FIN) AF: 0.0118 AC: 125 AN: 10604

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00634 AC: 431 AN: 68008

Other (OTH) AF: 0.0213 AC: 45 AN: 2112

Alfa AF: 0.0153 Hom.: 9

Bravo AF: 0.0216

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.74
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10491302; hg19: chr5-136301472;