14-40493784-T-C

Position:

• chr14-40493784-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 0.952 in 152,264 control chromosomes in the GnomAD database, including 69,108 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 0.95 (69108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 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: 0.952 AC: 144895 AN: 152146 Hom.: 69051 Cov.: 32

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.959

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

GnomAD4 genome AF: 0.952 AC: 145011 AN: 152264 Hom.: 69108 Cov.: 32 AF XY: 0.953 AC XY: 70939 AN XY: 74444

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.966

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.959

Alfa AF: 0.939 Hom.: 7814

Bravo AF: 0.956

Asia WGS AF: 0.990 AC: 3443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1888588; hg19: chr14-40962988;