rs1015820

Positions:

• chr18-77184858-G-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, non coding transcript 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: ENST00000584843.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000584843.1	n.96-326G>A		intron_variant, non_coding_transcript_variant		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;