chr14-24498246-G-T

Variant names:

• chr14-24498246-G-T
• rs17184822
• ENST00000555109.2:n.375-3314G>T

Variant summary

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

The ENST00000555109.2(ENSG00000258744):​n.375-3314G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,098 control chromosomes in the GnomAD database, including 2,132 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 0.15 (2132 hom., cov: 32)
• Consequence: ENSG00000258744 ENST00000555109.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927045	NR_110032.1	n.1479-3314G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258744	ENST00000555109.2	n.375-3314G>T		intron_variant	Intron 2 of 3	5
ENSG00000258744	ENST00000656888.2	n.304-3314G>T		intron_variant	Intron 2 of 2
ENSG00000258744	ENST00000816252.1	n.263-3314G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23003 AN: 151980 Hom.: 2129 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.151 AC: 23038 AN: 152098 Hom.: 2132 Cov.: 32 AF XY: 0.149 AC XY: 11101 AN XY: 74356

African (AFR) AF: 0.242 AC: 10052 AN: 41452

American (AMR) AF: 0.138 AC: 2113 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1723 AN: 5160

South Asian (SAS) AF: 0.173 AC: 832 AN: 4820

European-Finnish (FIN) AF: 0.0594 AC: 629 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6923 AN: 67992

Other (OTH) AF: 0.152 AC: 320 AN: 2106

Alfa AF: 0.126 Hom.: 993

Bravo AF: 0.162

Asia WGS AF: 0.285 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs17184822; hg19: chr14-24967452;