13-77679067-T-C

Variant names:

• chr13-77679067-T-C
• rs1937388

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 0.821 in 151,838 control chromosomes in the GnomAD database, including 51,825 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 0.82 (51825 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.886 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: 0.822 AC: 124686 AN: 151720 Hom.: 51815 Cov.: 28

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.821 AC: 124732 AN: 151838 Hom.: 51825 Cov.: 28 AF XY: 0.823 AC XY: 61013 AN XY: 74174

African (AFR) AF: 0.677 AC: 28002 AN: 41378

American (AMR) AF: 0.895 AC: 13652 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2971 AN: 3468

East Asian (EAS) AF: 0.877 AC: 4477 AN: 5106

South Asian (SAS) AF: 0.909 AC: 4358 AN: 4796

European-Finnish (FIN) AF: 0.838 AC: 8843 AN: 10558

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59563 AN: 67956

Other (OTH) AF: 0.829 AC: 1752 AN: 2114

Alfa AF: 0.864 Hom.: 98480

Bravo AF: 0.820

Asia WGS AF: 0.879 AC: 3056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1937388; hg19: chr13-78253202;