14-61667038-C-T

Variant names:

• chr14-61667038-C-T
• rs2783778

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 0.58 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
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.186 AC: 7709 AN: 41484

American (AMR) AF: 0.684 AC: 10439 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3133 AN: 5168

South Asian (SAS) AF: 0.606 AC: 2921 AN: 4820

European-Finnish (FIN) AF: 0.877 AC: 9298 AN: 10602

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50656 AN: 67974

Other (OTH) AF: 0.571 AC: 1205 AN: 2110

Alfa AF: 0.686 Hom.: 61225

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2783778; hg19: chr14-62133756;