14-49908788-C-T

Variant names:

• chr14-49908788-C-T
• rs10140366

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 0.869 in 152,094 control chromosomes in the GnomAD database, including 57,528 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 0.87 (57528 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.917 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: 0.869 AC: 132064 AN: 151976 Hom.: 57478 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.869 AC: 132172 AN: 152094 Hom.: 57528 Cov.: 31 AF XY: 0.871 AC XY: 64755 AN XY: 74356

African (AFR) AF: 0.822 AC: 34082 AN: 41464

American (AMR) AF: 0.904 AC: 13820 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2998 AN: 3470

East Asian (EAS) AF: 0.939 AC: 4846 AN: 5160

South Asian (SAS) AF: 0.916 AC: 4418 AN: 4822

European-Finnish (FIN) AF: 0.871 AC: 9215 AN: 10584

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59869 AN: 67996

Other (OTH) AF: 0.867 AC: 1832 AN: 2112

Alfa AF: 0.877 Hom.: 29244

Bravo AF: 0.869

Asia WGS AF: 0.925 AC: 3218 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	0.14
DANN	Benign	0.32
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10140366; hg19: chr14-50375506;