rs7913838

Positions:

• chr10-36310294-A-C

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 0.0615 in 152,024 control chromosomes in the GnomAD database, including 332 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 0.061 (332 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0689 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: 0.0615 AC: 9342 AN: 151906 Hom.: 333 Cov.: 31

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0320

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0615 AC: 9349 AN: 152024 Hom.: 332 Cov.: 31 AF XY: 0.0604 AC XY: 4492 AN XY: 74320

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.0387

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0320

Gnomad4 FIN AF: 0.0756

Gnomad4 NFE AF: 0.0706

Gnomad4 OTH AF: 0.0538

Alfa AF: 0.0632 Hom.: 291

Bravo AF: 0.0593

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7913838; hg19: chr10-36599222;