rs11915891

Variant names:

• chr3-193770712-T-C
• rs11915891
• ENST00000666648.1:n.1363A>G

Variant summary

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

The ENST00000666648.1(ENSG00000286624):​n.1363A>G 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 0.339 in 152,098 control chromosomes in the GnomAD database, including 9,260 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 0.34 (9260 hom., cov: 33)
• Consequence: ENSG00000286624 ENST00000666648.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

Genes affected

ENSG00000286624 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374282	XR_924838.4	n.*240A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286624	ENST00000666648.1	n.1363A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51431 AN: 151978 Hom.: 9237 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.339 AC: 51512 AN: 152098 Hom.: 9260 Cov.: 33 AF XY: 0.342 AC XY: 25444 AN XY: 74362

African (AFR) AF: 0.447 AC: 18561 AN: 41482

American (AMR) AF: 0.303 AC: 4629 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2470 AN: 5176

South Asian (SAS) AF: 0.488 AC: 2352 AN: 4822

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10578

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18776 AN: 67964

Other (OTH) AF: 0.320 AC: 675 AN: 2110

Alfa AF: 0.301 Hom.: 13349

Bravo AF: 0.342

Asia WGS AF: 0.482 AC: 1656 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.70
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11915891; hg19: chr3-193488501;