ENST00000665870.1:n.3232C>T

Variant names:

• chr6-285695-G-A
• rs815583
• ENST00000665870.1:n.3232C>T

Variant summary

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

The ENST00000665870.1(ENSG00000287265):​n.3232C>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 0.78 in 152,146 control chromosomes in the GnomAD database, including 43,201 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 0.78 (43201 hom., cov: 51)
• Consequence: ENSG00000287265 ENST00000665870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 5 publications found

Genes affected

ENSG00000287265 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665870.1. 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
	ENSG00000287265	ENST00000665870.1		n.3232C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118555 AN: 152028 Hom.: 43159 Cov.: 51

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.780 AC: 118657 AN: 152146 Hom.: 43201 Cov.: 51 AF XY: 0.782 AC XY: 58198 AN XY: 74382

African (AFR) AF: 0.670 AC: 27776 AN: 41448

American (AMR) AF: 0.860 AC: 13160 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2768 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4492 AN: 5186

South Asian (SAS) AF: 0.809 AC: 3905 AN: 4826

European-Finnish (FIN) AF: 0.820 AC: 8692 AN: 10604

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55212 AN: 67998

Other (OTH) AF: 0.787 AC: 1662 AN: 2112

Alfa AF: 0.800 Hom.: 6737

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs815583; hg19: chr6-285695;