chr13-80594266-G-C

Variant names:

• chr13-80594266-G-C
• rs10507907

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.170 AC: 7055 AN: 41388

American (AMR) AF: 0.0352 AC: 537 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 237 AN: 3462

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5160

South Asian (SAS) AF: 0.0185 AC: 89 AN: 4818

European-Finnish (FIN) AF: 0.00408 AC: 43 AN: 10544

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0232 AC: 1576 AN: 67908

Other (OTH) AF: 0.0564 AC: 119 AN: 2110

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10507907; hg19: chr13-81168401;