13-26928142-T-C

Variant names:

• chr13-26928142-T-C
• rs1576168

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 0.64 in 151,962 control chromosomes in the GnomAD database, including 31,585 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 0.64 (31585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 6 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 = 0.95 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97127 AN: 151844 Hom.: 31565 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.640 AC: 97193 AN: 151962 Hom.: 31585 Cov.: 32 AF XY: 0.645 AC XY: 47926 AN XY: 74280

African (AFR) AF: 0.625 AC: 25913 AN: 41438

American (AMR) AF: 0.726 AC: 11098 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2238 AN: 3468

East Asian (EAS) AF: 0.973 AC: 5039 AN: 5180

South Asian (SAS) AF: 0.645 AC: 3095 AN: 4802

European-Finnish (FIN) AF: 0.647 AC: 6806 AN: 10522

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41119 AN: 67956

Other (OTH) AF: 0.631 AC: 1332 AN: 2112

Alfa AF: 0.623 Hom.: 56935

Bravo AF: 0.649

Asia WGS AF: 0.804 AC: 2795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs1576168; hg19: chr13-27502279;