rs1015834

chr18-29327451-A-T

Variant summary

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

The ENST00000577674.1(ENSG00000265980):n.80+34433T>A variant causes a intron, non coding transcript 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: ENST00000577674.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000577674.1	n.80+34433T>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.0651

Gnomad4 ASJ AF: 0.0735

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0938

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015834; hg19: chr18-26907416;