rs10507907

Variant names:

• chr13-80594266-G-C
• rs10507907

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 0.064 in 151,838 control chromosomes in the GnomAD database, including 604 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 0.064 (604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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: 0.0640 AC: 9706 AN: 151720 Hom.: 606 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0185

Gnomad FIN AF: 0.00408

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0640 AC: 9722 AN: 151838 Hom.: 604 Cov.: 32 AF XY: 0.0610 AC XY: 4531 AN XY: 74220

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0185

Gnomad4 FIN AF: 0.00408

Gnomad4 NFE AF: 0.0232

Gnomad4 OTH AF: 0.0564

Alfa AF: 0.0442 Hom.: 47

Bravo AF: 0.0704

Asia WGS AF: 0.0220 AC: 79 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507907; hg19: chr13-81168401;