14-61674004-C-G

Position:

• chr14-61674004-C-G

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 0.709 in 152,222 control chromosomes in the GnomAD database, including 44,517 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 0.71 (44517 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107889 AN: 152104 Hom.: 44511 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.709 AC: 107927 AN: 152222 Hom.: 44517 Cov.: 33 AF XY: 0.716 AC XY: 53271 AN XY: 74440

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.733

Alfa AF: 0.790 Hom.: 6451

Bravo AF: 0.682

Asia WGS AF: 0.782 AC: 2718 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256605; hg19: chr14-62140722;