rs10491302

chr5-136965783-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 92 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.0128

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0211

Gnomad4 SAS AF: 0.0398

Gnomad4 FIN AF: 0.0118

Gnomad4 NFE AF: 0.00634

Gnomad4 OTH AF: 0.0213

Alfa AF: 0.0143 Hom.: 8

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491302; hg19: chr5-136301472;