rs11059374

Variant names:

• chr12-127819873-C-T
• rs11059374
• ENST00000541797.1:n.172+1139G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000541797.1(ENSG00000286662):​n.172+1139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,198 control chromosomes in the GnomAD database, including 2,408 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 0.16 (2408 hom., cov: 32)
• Consequence: ENSG00000286662 ENST00000541797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

Genes affected

ENSG00000286662 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286662	ENST00000541797.1	n.172+1139G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24083 AN: 152080 Hom.: 2407 Cov.: 32

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.158 AC: 24082 AN: 152198 Hom.: 2408 Cov.: 32 AF XY: 0.162 AC XY: 12037 AN XY: 74398

Gnomad4 AFR AF: 0.0418

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.144

Alfa AF: 0.191 Hom.: 3380

Bravo AF: 0.151

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11059374; hg19: chr12-128304418;