rs1511453

Variant names:

• chr4-23586839-G-A
• rs1511453
• ENST00000514290.1:n.117+25800G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-23586839-G-A
• chr4-23586839-G-C
• chr4-23586839-G-T

Variant summary

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

The ENST00000514290.1(ENSG00000250137):​n.117+25800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0929 in 152,064 control chromosomes in the GnomAD database, including 797 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 0.093 (797 hom., cov: 33)
• Consequence: ENSG00000250137 ENST00000514290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 4 publications found

Genes affected

ENSG00000250137 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 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
ENSG00000250137	ENST00000514290.1	n.117+25800G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14106 AN: 151944 Hom.: 791 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0929

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

GnomAD4 genome AF: 0.0929 AC: 14120 AN: 152064 Hom.: 797 Cov.: 33 AF XY: 0.0948 AC XY: 7043 AN XY: 74326

African (AFR) AF: 0.112 AC: 4641 AN: 41472

American (AMR) AF: 0.141 AC: 2150 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1051 AN: 5148

South Asian (SAS) AF: 0.109 AC: 526 AN: 4814

European-Finnish (FIN) AF: 0.0603 AC: 638 AN: 10588

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0643 AC: 4374 AN: 67994

Other (OTH) AF: 0.0910 AC: 192 AN: 2110

Alfa AF: 0.0909 Hom.: 552

Bravo AF: 0.103

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.83
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1511453; hg19: chr4-23588462;