13-75982273-C-T

Variant names:

• chr13-75982273-C-T
• rs1870836

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 0.611 in 151,786 control chromosomes in the GnomAD database, including 28,561 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 0.61 (28561 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92646 AN: 151668 Hom.: 28533 Cov.: 29

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.611 AC: 92736 AN: 151786 Hom.: 28561 Cov.: 29 AF XY: 0.612 AC XY: 45392 AN XY: 74174

African (AFR) AF: 0.559 AC: 23117 AN: 41362

American (AMR) AF: 0.609 AC: 9276 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1744 AN: 3460

East Asian (EAS) AF: 0.480 AC: 2467 AN: 5140

South Asian (SAS) AF: 0.511 AC: 2455 AN: 4808

European-Finnish (FIN) AF: 0.676 AC: 7138 AN: 10554

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.656 AC: 44567 AN: 67912

Other (OTH) AF: 0.582 AC: 1229 AN: 2112

Alfa AF: 0.628 Hom.: 3724

Bravo AF: 0.602

Asia WGS AF: 0.539 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.10
DANN	Benign	0.57
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1870836; hg19: chr13-76556409;