13-85281999-A-G

Variant names:

• chr13-85281999-A-G
• rs10507949

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 0.0792 in 152,068 control chromosomes in the GnomAD database, including 951 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 0.079 (951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.345 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: 0.0791 AC: 12023 AN: 151952 Hom.: 948 Cov.: 32

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0792 AC: 12042 AN: 152068 Hom.: 951 Cov.: 32 AF XY: 0.0866 AC XY: 6437 AN XY: 74342

African (AFR) AF: 0.0796 AC: 3309 AN: 41548

American (AMR) AF: 0.183 AC: 2784 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1848 AN: 5152

South Asian (SAS) AF: 0.0908 AC: 438 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1114 AN: 10598

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0313 AC: 2128 AN: 67946

Other (OTH) AF: 0.0832 AC: 175 AN: 2104

Alfa AF: 0.0660 Hom.: 220

Bravo AF: 0.0904

Asia WGS AF: 0.226 AC: 778 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.47
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10507949; hg19: chr13-85856134;