rs585811

Variant names:

• chr18-79779764-C-A
• rs585811
• ENST00000805936.1:n.147G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-79779764-C-A
• chr18-79779764-C-T

Variant summary

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

The ENST00000805936.1(ENSG00000304742):​n.147G>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 0.464 in 152,132 control chromosomes in the GnomAD database, including 19,207 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 0.46 (19207 hom., cov: 34)
• Consequence: ENSG00000304742 ENST00000805936.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 2 publications found

Genes affected

ENSG00000304742 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805936.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304742	ENST00000805936.1		n.147G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000304742	ENST00000805935.1		n.195-392G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70587 AN: 152014 Hom.: 19205 Cov.: 34

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.464 AC: 70604 AN: 152132 Hom.: 19207 Cov.: 34 AF XY: 0.465 AC XY: 34607 AN XY: 74346

African (AFR) AF: 0.165 AC: 6849 AN: 41536

American (AMR) AF: 0.484 AC: 7404 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1817 AN: 3472

East Asian (EAS) AF: 0.543 AC: 2806 AN: 5168

South Asian (SAS) AF: 0.611 AC: 2946 AN: 4824

European-Finnish (FIN) AF: 0.612 AC: 6467 AN: 10570

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40576 AN: 67954

Other (OTH) AF: 0.502 AC: 1062 AN: 2116

Alfa AF: 0.550 Hom.: 40254

Bravo AF: 0.437

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.69
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs585811; hg19: chr18-77539764;