13-77679067-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.829

Alfa AF: 0.870 Hom.: 79407

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1937388; hg19: chr13-78253202;