rs1156044

Variant names:

• chr18-9102142-G-A
• rs1156044
• ENST00000688917.1:n.351C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-9102142-G-A
• chr18-9102142-G-C
• chr18-9102142-G-T

Variant summary

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

The ENST00000688917.1(ENSG00000288939):​n.351C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 151,984 control chromosomes in the GnomAD database, including 50,705 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 0.82 (50705 hom., cov: 29)
• Consequence: ENSG00000288939 ENST00000688917.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

ENSG00000288939 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 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
ENSG00000288939	ENST00000688917.1	n.351C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123913 AN: 151866 Hom.: 50659 Cov.: 29

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.816 AC: 124012 AN: 151984 Hom.: 50705 Cov.: 29 AF XY: 0.813 AC XY: 60377 AN XY: 74282

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.833

Alfa AF: 0.835 Hom.: 58712

Bravo AF: 0.814

Asia WGS AF: 0.750 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.79
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1156044; hg19: chr18-9102140;