rs1015834

Variant names:

• chr18-29327451-A-T
• rs1015834
• ENST00000577674.1:n.80+34433T>A

Variant summary

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

The ENST00000577674.1(ENSG00000265980):​n.80+34433T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0849 in 152,150 control chromosomes in the GnomAD database, including 746 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 0.085 (746 hom., cov: 32)
• Consequence: ENSG00000265980 ENST00000577674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 0 publications found

Genes affected

ENSG00000265980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577674.1. 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
	ENSG00000265980	ENST00000577674.1	TSL:3	n.80+34433T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12915 AN: 152032 Hom.: 746 Cov.: 32

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.0849 AC: 12910 AN: 152150 Hom.: 746 Cov.: 32 AF XY: 0.0838 AC XY: 6235 AN XY: 74376

African (AFR) AF: 0.0246 AC: 1024 AN: 41542

American (AMR) AF: 0.0651 AC: 994 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.0236 AC: 114 AN: 4826

European-Finnish (FIN) AF: 0.135 AC: 1430 AN: 10580

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8759 AN: 67978

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.105 Hom.: 128

Bravo AF: 0.0777

Asia WGS AF: 0.0140 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.78
PhyloP100		0.42

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: rs1015834;

hg19: chr18-26907416;