chr10-5291045-G-A

Position:

• chr10-5291045-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.633 in 152,084 control chromosomes in the GnomAD database, including 30,855 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 0.63 (30855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96163 AN: 151966 Hom.: 30821 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.633 AC: 96255 AN: 152084 Hom.: 30855 Cov.: 32 AF XY: 0.636 AC XY: 47256 AN XY: 74344

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.607

Alfa AF: 0.597 Hom.: 49102

Bravo AF: 0.630

Asia WGS AF: 0.768 AC: 2671 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	0.95
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7076488; hg19: chr10-5333008;