14-24779087-G-C

Variant names:

• chr14-24779087-G-C
• rs17795514

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 0.377 in 151,904 control chromosomes in the GnomAD database, including 12,863 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 0.38 (12863 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 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: 0.377 AC: 57298 AN: 151786 Hom.: 12871 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.377 AC: 57299 AN: 151904 Hom.: 12863 Cov.: 31 AF XY: 0.381 AC XY: 28281 AN XY: 74216

African (AFR) AF: 0.127 AC: 5254 AN: 41464

American (AMR) AF: 0.487 AC: 7425 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1334 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1247 AN: 5154

South Asian (SAS) AF: 0.415 AC: 1991 AN: 4796

European-Finnish (FIN) AF: 0.495 AC: 5214 AN: 10538

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33560 AN: 67930

Other (OTH) AF: 0.379 AC: 800 AN: 2110

Alfa AF: 0.299 Hom.: 865

Bravo AF: 0.367

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.51
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs17795514; hg19: chr14-25248293;