13-73084116-T-G

Variant names:

• chr13-73084116-T-G
• rs12869881

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 0.226 in 149,888 control chromosomes in the GnomAD database, including 4,094 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 0.23 (4094 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 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: 0.226 AC: 33877 AN: 149816 Hom.: 4094 Cov.: 30

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.226 AC: 33901 AN: 149888 Hom.: 4094 Cov.: 30 AF XY: 0.228 AC XY: 16643 AN XY: 72942

African (AFR) AF: 0.317 AC: 12913 AN: 40686

American (AMR) AF: 0.223 AC: 3335 AN: 14966

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3460

East Asian (EAS) AF: 0.234 AC: 1190 AN: 5078

South Asian (SAS) AF: 0.230 AC: 1101 AN: 4784

European-Finnish (FIN) AF: 0.226 AC: 2242 AN: 9908

Middle Eastern (MID) AF: 0.168 AC: 48 AN: 286

European-Non Finnish (NFE) AF: 0.177 AC: 11958 AN: 67748

Other (OTH) AF: 0.224 AC: 462 AN: 2064

Alfa AF: 0.190 Hom.: 8740

Bravo AF: 0.232

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.68
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs12869881; hg19: chr13-73658254;