14-24484796-T-C

Variant names:

• chr14-24484796-T-C
• rs2877649
• ENST00000555109.2:n.375-16764T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555109.2(ENSG00000258744):​n.375-16764T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,216 control chromosomes in the GnomAD database, including 59,716 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 0.88 (59716 hom., cov: 33)
• Consequence: ENSG00000258744 ENST00000555109.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 7 publications found

Genes affected

ENSG00000258744 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927045	NR_110032.1	n.1479-16764T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258744	ENST00000555109.2	n.375-16764T>C		intron_variant	Intron 2 of 3	5
ENSG00000258744	ENST00000656888.2	n.304-16764T>C		intron_variant	Intron 2 of 2
ENSG00000258744	ENST00000816252.1	n.262+2706T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133117 AN: 152098 Hom.: 59676 Cov.: 33

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.875 AC: 133212 AN: 152216 Hom.: 59716 Cov.: 33 AF XY: 0.878 AC XY: 65354 AN XY: 74428

African (AFR) AF: 0.660 AC: 27371 AN: 41464

American (AMR) AF: 0.909 AC: 13907 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3350 AN: 3472

East Asian (EAS) AF: 0.870 AC: 4515 AN: 5188

South Asian (SAS) AF: 0.926 AC: 4466 AN: 4822

European-Finnish (FIN) AF: 0.971 AC: 10306 AN: 10612

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66225 AN: 68034

Other (OTH) AF: 0.895 AC: 1891 AN: 2114

Alfa AF: 0.947 Hom.: 109949

Bravo AF: 0.862

Asia WGS AF: 0.856 AC: 2978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.55
DANN	Benign	0.41
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2877649; hg19: chr14-24954002;