rs17287293

Variant names:

• chr12-24617944-A-G
• rs17287293
• ENST00000741714.1:n.372-134T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000741714.1(ENSG00000296761):​n.372-134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,256 control chromosomes in the GnomAD database, including 1,333 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 0.12 (1333 hom., cov: 33)
• Consequence: ENSG00000296761 ENST00000741714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 34 publications found

Genes affected

ENSG00000296761 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369698	XR_001749046.2	n.327-134T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296761	ENST00000741714.1	n.372-134T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18486 AN: 152138 Hom.: 1331 Cov.: 33

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.121 AC: 18496 AN: 152256 Hom.: 1333 Cov.: 33 AF XY: 0.122 AC XY: 9084 AN XY: 74440

African (AFR) AF: 0.0457 AC: 1899 AN: 41544

American (AMR) AF: 0.163 AC: 2499 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3470

East Asian (EAS) AF: 0.129 AC: 671 AN: 5182

South Asian (SAS) AF: 0.256 AC: 1234 AN: 4818

European-Finnish (FIN) AF: 0.105 AC: 1112 AN: 10618

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10019 AN: 68012

Other (OTH) AF: 0.148 AC: 313 AN: 2114

Alfa AF: 0.144 Hom.: 6343

Bravo AF: 0.122

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs17287293; hg19: chr12-24770878;