ENST00000718672.1:n.705G>A

Variant names:

• chr20-23511141-C-T
• rs6076080
• ENST00000718672.1:n.705G>A

Variant summary

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

The ENST00000718672.1(ENSG00000260202):​n.705G>A 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 0.0817 in 152,252 control chromosomes in the GnomAD database, including 682 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 0.082 (682 hom., cov: 33)
• Consequence: ENSG00000260202 ENST00000718672.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 2 publications found

Genes affected

ENSG00000260202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718672.1. 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
	ENSG00000260202	ENST00000718672.1		n.705G>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000260202	ENST00000619495.1	TSL:4	n.438+7476G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0817 AC: 12432 AN: 152134 Hom.: 680 Cov.: 33

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0817 AC: 12438 AN: 152252 Hom.: 682 Cov.: 33 AF XY: 0.0818 AC XY: 6089 AN XY: 74446

African (AFR) AF: 0.0242 AC: 1004 AN: 41548

American (AMR) AF: 0.131 AC: 2008 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3472

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5176

South Asian (SAS) AF: 0.0704 AC: 340 AN: 4830

European-Finnish (FIN) AF: 0.101 AC: 1065 AN: 10596

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7444 AN: 68008

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0980 Hom.: 815

Bravo AF: 0.0835

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.79
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6076080;

hg19: chr20-23491778;