14-42150058-G-C

Variant names:

• chr14-42150058-G-C
• rs1954627

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 0.737 in 152,018 control chromosomes in the GnomAD database, including 41,336 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 0.74 (41336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.737 AC: 111971 AN: 151900 Hom.: 41303 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.737 AC: 112063 AN: 152018 Hom.: 41336 Cov.: 32 AF XY: 0.740 AC XY: 55003 AN XY: 74302

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.735

Alfa AF: 0.726 Hom.: 4715

Bravo AF: 0.733

Asia WGS AF: 0.790 AC: 2746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1954627; hg19: chr14-42619261;