ENST00000392097.6:n.10688G>A

Variant names:

• chr1-169496759-G-A
• rs723751
• ENST00000392097.6:n.10688G>A

Variant summary

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

The ENST00000392097.6(ENSG00000213062):​n.10688G>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 0.272 in 151,964 control chromosomes in the GnomAD database, including 5,735 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 0.27 (5735 hom., cov: 31)
• Consequence: ENSG00000213062 ENST00000392097.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 4 publications found

Genes affected

ENSG00000213062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000213062	ENST00000392097.6	n.10688G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41312 AN: 151846 Hom.: 5724 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.272 AC: 41339 AN: 151964 Hom.: 5735 Cov.: 31 AF XY: 0.272 AC XY: 20184 AN XY: 74276

African (AFR) AF: 0.294 AC: 12177 AN: 41424

American (AMR) AF: 0.337 AC: 5140 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 581 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5168

South Asian (SAS) AF: 0.383 AC: 1845 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2139 AN: 10558

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17650 AN: 67952

Other (OTH) AF: 0.258 AC: 545 AN: 2112

Alfa AF: 0.270 Hom.: 9527

Bravo AF: 0.282

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.16
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs723751; hg19: chr1-169465997;