rs10491303

chr5-136890859-A-G

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 0.025 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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 98 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: 0.0250 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

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.0176

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.0265

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.00875

Gnomad4 NFE AF: 0.0131

Gnomad4 OTH AF: 0.0228

Alfa AF: 0.0188 Hom.: 17

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491303; hg19: chr5-136226548;