rs7076488

Variant names:

• chr10-5291045-G-A
• rs7076488

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;