11-60841460-C-A

Variant names:

• chr11-60841460-C-A
• rs561285
• ENST00000539897.1:n.349+1157G>T

Variant summary

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

The ENST00000539897.1(ENSG00000255959):​n.349+1157G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,004 control chromosomes in the GnomAD database, including 10,868 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 0.37 (10868 hom., cov: 32)
• Consequence: ENSG00000255959 ENST00000539897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

Genes affected

ENSG00000255959 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.406 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
ENSG00000255959	ENST00000539897.1	n.349+1157G>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56524 AN: 151882 Hom.: 10848 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.372 AC: 56598 AN: 152004 Hom.: 10868 Cov.: 32 AF XY: 0.366 AC XY: 27216 AN XY: 74302

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.401

Alfa AF: 0.394 Hom.: 1147

Bravo AF: 0.376

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs561285; hg19: chr11-60608933;