rs2783778

chr14-61667038-C-T

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 0.58 in 152,100 control chromosomes in the GnomAD database, including 30,556 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 0.58 (30556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.74 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: 0.580 AC: 88127 AN: 151982 Hom.: 30546 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.580 AC: 88150 AN: 152100 Hom.: 30556 Cov.: 32 AF XY: 0.587 AC XY: 43675 AN XY: 74352

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.571

Alfa AF: 0.704 Hom.: 49805

Bravo AF: 0.548

Asia WGS AF: 0.612 AC: 2128 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	0.28
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2783778; hg19: chr14-62133756;