rs584109

Variant names:

• chr11-94279588-G-T
• rs584109
• ENST00000515097.3:n.1276G>T

Variant summary

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

The ENST00000515097.3(ENSG00000250519):​n.1276G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,990 control chromosomes in the GnomAD database, including 14,898 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 0.42 (14898 hom., cov: 33)
• Consequence: ENSG00000250519 ENST00000515097.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 4 publications found

Genes affected

ENSG00000250519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369435	XR_947901.3	n.3882G>T		non_coding_transcript_exon_variant	Exon 5 of 5
LOC105369435	XR_947903.3	n.1334G>T		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250519	ENST00000515097.3	n.1276G>T		non_coding_transcript_exon_variant	Exon 2 of 2	4
ENSG00000250519	ENST00000663963.1	n.1078G>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000250519	ENST00000506309.7	n.*20G>T		downstream_gene_variant		4
ENSG00000250519	ENST00000655054.1	n.*15G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63327 AN: 151870 Hom.: 14880 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.417 AC: 63364 AN: 151990 Hom.: 14898 Cov.: 33 AF XY: 0.416 AC XY: 30920 AN XY: 74288

African (AFR) AF: 0.217 AC: 8981 AN: 41474

American (AMR) AF: 0.567 AC: 8666 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1062 AN: 5162

South Asian (SAS) AF: 0.246 AC: 1185 AN: 4820

European-Finnish (FIN) AF: 0.516 AC: 5442 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34626 AN: 67916

Other (OTH) AF: 0.477 AC: 1004 AN: 2106

Alfa AF: 0.420 Hom.: 2218

Bravo AF: 0.420

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs584109; hg19: chr11-94012754;