rs7904954

Variant names:

• chr10-79999239-A-G
• rs7904954

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 0.636 in 152,178 control chromosomes in the GnomAD database, including 31,199 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 0.64 (31199 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 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: 0.636 AC: 96670 AN: 152060 Hom.: 31153 Cov.: 34

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.636 AC: 96775 AN: 152178 Hom.: 31199 Cov.: 34 AF XY: 0.636 AC XY: 47328 AN XY: 74398

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.631

Alfa AF: 0.602 Hom.: 56060

Bravo AF: 0.639

Asia WGS AF: 0.734 AC: 2551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7904954; hg19: chr10-81758995;