rs2117047

Variant names:

• chr12-76003767-G-A
• rs2117047
• ENST00000813167.1:n.184-345C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-76003767-G-A
• chr12-76003767-G-T

Variant summary

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

The ENST00000813167.1(ENSG00000305824):​n.184-345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,874 control chromosomes in the GnomAD database, including 19,281 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 0.50 (19281 hom., cov: 31)
• Consequence: ENSG00000305824 ENST00000813167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 2 publications found

Genes affected

ENSG00000305824 (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 = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369847	XR_945110.4	n.403-345C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305824	ENST00000813167.1	n.184-345C>T		intron_variant	Intron 2 of 3
ENSG00000305824	ENST00000813168.1	n.268-345C>T		intron_variant	Intron 1 of 2
ENSG00000257329	ENST00000813228.1	n.580-1794G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76161 AN: 151754 Hom.: 19283 Cov.: 31

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.502 AC: 76170 AN: 151874 Hom.: 19281 Cov.: 31 AF XY: 0.503 AC XY: 37316 AN XY: 74196

African (AFR) AF: 0.475 AC: 19644 AN: 41390

American (AMR) AF: 0.486 AC: 7415 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2414 AN: 3472

East Asian (EAS) AF: 0.387 AC: 1997 AN: 5160

South Asian (SAS) AF: 0.637 AC: 3065 AN: 4814

European-Finnish (FIN) AF: 0.516 AC: 5429 AN: 10522

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34293 AN: 67954

Other (OTH) AF: 0.545 AC: 1148 AN: 2108

Alfa AF: 0.504 Hom.: 16485

Bravo AF: 0.495

Asia WGS AF: 0.561 AC: 1953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.77
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2117047; hg19: chr12-76397547;