ENST00000556386.2:n.349-15512G>A

Variant names:

• chr14-95739733-G-A
• rs2369304
• ENST00000556386.2:n.349-15512G>A

Variant summary

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

The ENST00000556386.2(ENSG00000257275):​n.349-15512G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,012 control chromosomes in the GnomAD database, including 18,767 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 0.46 (18767 hom., cov: 32)
• Consequence: ENSG00000257275 ENST00000556386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 5 publications found

Genes affected

ENSG00000257275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984703	NR_148060.1	n.324-15512G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257275	ENST00000556386.2	n.349-15512G>A		intron_variant	Intron 2 of 2	1
ENSG00000257275	ENST00000547644.6	n.251-15512G>A		intron_variant	Intron 2 of 2	2
ENSG00000257275	ENST00000553445.5	n.368-15512G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69401 AN: 151894 Hom.: 18720 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.457 AC: 69502 AN: 152012 Hom.: 18767 Cov.: 32 AF XY: 0.457 AC XY: 33964 AN XY: 74280

African (AFR) AF: 0.766 AC: 31752 AN: 41450

American (AMR) AF: 0.366 AC: 5595 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1164 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1695 AN: 5176

South Asian (SAS) AF: 0.358 AC: 1723 AN: 4812

European-Finnish (FIN) AF: 0.450 AC: 4744 AN: 10550

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21698 AN: 67976

Other (OTH) AF: 0.408 AC: 860 AN: 2108

Alfa AF: 0.370 Hom.: 21657

Bravo AF: 0.464

Asia WGS AF: 0.382 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.56
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2369304; hg19: chr14-96206070;