ENST00000731692.1:n.81T>C

Variant names:

• chr8-102627713-T-C
• rs6998277
• ENST00000731692.1:n.81T>C

Variant summary

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

The ENST00000731692.1(ENSG00000283959):​n.81T>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 0.262 in 152,022 control chromosomes in the GnomAD database, including 6,238 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 0.26 (6238 hom., cov: 32)
• Consequence: ENSG00000283959 ENST00000731692.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 11 publications found

Genes affected

ENSG00000283959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731692.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283959	ENST00000731692.1		n.81T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000283959	ENST00000731667.1		n.-114T>C		upstream_gene	N/A
	ENSG00000283959	ENST00000731685.1		n.-48T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39817 AN: 151904 Hom.: 6220 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.262 AC: 39887 AN: 152022 Hom.: 6238 Cov.: 32 AF XY: 0.259 AC XY: 19221 AN XY: 74318

African (AFR) AF: 0.444 AC: 18397 AN: 41442

American (AMR) AF: 0.191 AC: 2917 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 550 AN: 3472

East Asian (EAS) AF: 0.160 AC: 829 AN: 5166

South Asian (SAS) AF: 0.214 AC: 1029 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2009 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13465 AN: 67960

Other (OTH) AF: 0.231 AC: 487 AN: 2108

Alfa AF: 0.210 Hom.: 4393

Bravo AF: 0.267

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs6998277; hg19: chr8-103639941;