rs1015820

Variant names:

• chr18-77184858-G-A
• rs1015820
• ENST00000584843.1:n.96-326G>A

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.96-326G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,080 control chromosomes in the GnomAD database, including 13,842 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 0.41 (13842 hom., cov: 32)
• Consequence: ENSG00000265844 ENST00000584843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 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
ENSG00000265844	ENST00000584843.1	n.96-326G>A		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61783 AN: 151962 Hom.: 13840 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.406 AC: 61781 AN: 152080 Hom.: 13842 Cov.: 32 AF XY: 0.405 AC XY: 30089 AN XY: 74308

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.425

Alfa AF: 0.491 Hom.: 34356

Bravo AF: 0.399

Asia WGS AF: 0.414 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015820; hg19: chr18-74896814;