rs11080702

Variant names:

• chr18-13943769-G-A
• rs11080702
• ENST00000728260.1:n.487-5147C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-13943769-G-A
• chr18-13943769-G-C

Variant summary

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

The ENST00000728260.1(ENSG00000295149):​n.487-5147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,158 control chromosomes in the GnomAD database, including 49,790 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 0.80 (49790 hom., cov: 32)
• Consequence: ENSG00000295149 ENST00000728260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 3 publications found

Genes affected

ENSG00000295149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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
ENSG00000295149	ENST00000728260.1	n.487-5147C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121682 AN: 152040 Hom.: 49772 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.800 AC: 121734 AN: 152158 Hom.: 49790 Cov.: 32 AF XY: 0.805 AC XY: 59909 AN XY: 74412

African (AFR) AF: 0.618 AC: 25581 AN: 41424

American (AMR) AF: 0.872 AC: 13330 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2740 AN: 3470

East Asian (EAS) AF: 0.980 AC: 5092 AN: 5194

South Asian (SAS) AF: 0.939 AC: 4526 AN: 4822

European-Finnish (FIN) AF: 0.883 AC: 9367 AN: 10604

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58413 AN: 68030

Other (OTH) AF: 0.803 AC: 1697 AN: 2114

Alfa AF: 0.823 Hom.: 9092

Bravo AF: 0.790

Asia WGS AF: 0.937 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.72
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs11080702; hg19: chr18-13943768;