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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666648.1. 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
	ENSG00000286624	ENST00000666648.1		n.1363A>G		non_coding_transcript_exon	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 v4.9

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

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

Other links and lift over

dbSNP: rs11915891;

hg19: chr3-193488501;