rs1290349

Variant names:

• chr11-112166831-C-A
• rs1290349
• ENST00000532699.1:n.315-3588C>A

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.315-3588C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,068 control chromosomes in the GnomAD database, including 5,045 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 0.25 (5045 hom., cov: 32)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 7 publications found

Genes affected

ENSG00000255292 (HGNC:):

ENSG00000254638 (HGNC:58436):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX12-AS1	XR_001748384.2	n.81+232G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255292	ENST00000532699.1	n.315-3588C>A		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.320-3588C>A		intron_variant	Intron 3 of 5	4
ENSG00000254638	ENST00000527589.1	n.171-655G>T		intron_variant	Intron 2 of 3	3
ENSG00000255292	ENST00000531744.5	n.315-3588C>A		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38427 AN: 151952 Hom.: 5046 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.253 AC: 38420 AN: 152068 Hom.: 5045 Cov.: 32 AF XY: 0.253 AC XY: 18800 AN XY: 74348

African (AFR) AF: 0.214 AC: 8867 AN: 41482

American (AMR) AF: 0.298 AC: 4561 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3466

East Asian (EAS) AF: 0.128 AC: 661 AN: 5174

South Asian (SAS) AF: 0.216 AC: 1044 AN: 4832

European-Finnish (FIN) AF: 0.287 AC: 3025 AN: 10548

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18522 AN: 67974

Other (OTH) AF: 0.245 AC: 516 AN: 2106

Alfa AF: 0.268 Hom.: 7022

Bravo AF: 0.253

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1290349; hg19: chr11-112037554;