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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515097.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250519	ENST00000515097.3	TSL:4	n.1276G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000250519	ENST00000663963.1		n.1078G>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000250519	ENST00000506309.7	TSL:4	n.*20G>T		downstream_gene	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs584109;

hg19: chr11-94012754;