chr14-41504140-T-C

Position:

• chr14-41504140-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 0.675 in 151,930 control chromosomes in the GnomAD database, including 35,472 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 0.68 (35472 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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 = 0.963 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: 0.675 AC: 102473 AN: 151812 Hom.: 35418 Cov.: 31

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.675 AC: 102591 AN: 151930 Hom.: 35472 Cov.: 31 AF XY: 0.678 AC XY: 50366 AN XY: 74272

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.635

Alfa AF: 0.618 Hom.: 12151

Bravo AF: 0.690

Asia WGS AF: 0.864 AC: 3002 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9285572; hg19: chr14-41973343;