rs1559759

Variant names:

• chr11-35101504-C-A
• rs1559759
• ENST00000747995.1:n.274+12929C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-35101504-C-A
• chr11-35101504-C-G
• chr11-35101504-C-T

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.274+12929C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,164 control chromosomes in the GnomAD database, including 1,896 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 0.15 (1896 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 10 publications found

Genes affected

ENSG00000297460 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747995.1. 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
	ENSG00000297460	ENST00000747995.1		n.274+12929C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22632 AN: 152046 Hom.: 1900 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.149 AC: 22628 AN: 152164 Hom.: 1896 Cov.: 32 AF XY: 0.152 AC XY: 11314 AN XY: 74378

African (AFR) AF: 0.126 AC: 5240 AN: 41522

American (AMR) AF: 0.102 AC: 1555 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3472

East Asian (EAS) AF: 0.324 AC: 1675 AN: 5166

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1344 AN: 10582

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10400 AN: 67984

Other (OTH) AF: 0.161 AC: 341 AN: 2112

Alfa AF: 0.155 Hom.: 8933

Bravo AF: 0.143

Asia WGS AF: 0.270 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		0.36

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: rs1559759;

hg19: chr11-35123051;