15-80770371-T-G

Variant names:

• chr15-80770371-T-G
• rs2660992
• ENST00000658807.1:n.1579A>C

Variant summary

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

The ENST00000658807.1(ENSG00000287108):​n.1579A>C 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 0.948 in 152,274 control chromosomes in the GnomAD database, including 68,402 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 0.95 (68402 hom., cov: 32)
• Consequence: ENSG00000287108 ENST00000658807.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 3 publications found

Genes affected

ENSG00000287108 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658807.1. 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
	ENSG00000287108	ENST00000658807.1		n.1579A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000287108	ENST00000721873.1		n.394+1308A>C		intron	N/A
	ENSG00000287108	ENST00000721874.1		n.606+1308A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.948 AC: 144186 AN: 152156 Hom.: 68342 Cov.: 32

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.948 AC: 144305 AN: 152274 Hom.: 68402 Cov.: 32 AF XY: 0.950 AC XY: 70738 AN XY: 74456

African (AFR) AF: 0.950 AC: 39456 AN: 41548

American (AMR) AF: 0.953 AC: 14581 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3180 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5037 AN: 5176

South Asian (SAS) AF: 0.909 AC: 4385 AN: 4822

European-Finnish (FIN) AF: 0.979 AC: 10391 AN: 10618

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64165 AN: 68032

Other (OTH) AF: 0.940 AC: 1981 AN: 2108

Alfa AF: 0.940 Hom.: 135739

Bravo AF: 0.946

Asia WGS AF: 0.942 AC: 3277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.3
DANN	Benign	0.41
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs2660992; hg19: chr15-81062712;