14-40493784-T-C

Variant names:

• chr14-40493784-T-C
• rs1888588

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 0.952 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.987 AC: 41025 AN: 41560

American (AMR) AF: 0.966 AC: 14761 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3309 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5170 AN: 5172

South Asian (SAS) AF: 0.989 AC: 4777 AN: 4828

European-Finnish (FIN) AF: 0.917 AC: 9730 AN: 10608

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63135 AN: 68028

Other (OTH) AF: 0.959 AC: 2024 AN: 2110

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
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs1888588; hg19: chr14-40962988;