rs561285

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-60841460-C-A
• chr11-60841460-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000255959 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539897.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255959	ENST00000539897.1	TSL:4	n.349+1157G>T		intron	N/A
	ENSG00000255959	ENST00000753859.1		n.396+1157G>T		intron	N/A
	ENSG00000255959	ENST00000753860.1		n.468+733G>T		intron	N/A

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

African (AFR) AF: 0.338 AC: 13994 AN: 41410

American (AMR) AF: 0.414 AC: 6331 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3470

East Asian (EAS) AF: 0.126 AC: 652 AN: 5190

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4816

European-Finnish (FIN) AF: 0.376 AC: 3962 AN: 10548

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27505 AN: 67978

Other (OTH) AF: 0.401 AC: 847 AN: 2110

Alfa AF: 0.396 Hom.: 12987

Bravo AF: 0.376

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs561285;

hg19: chr11-60608933;