ENST00000702750.2:n.209-313G>A

Variant names:

• chr6-131440537-C-T
• rs2078265
• ENST00000702750.2:n.209-313G>A

Variant summary

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

The ENST00000702750.2(ENSG00000290067):​n.209-313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,960 control chromosomes in the GnomAD database, including 18,272 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 0.42 (18272 hom., cov: 31)
• Consequence: ENSG00000290067 ENST00000702750.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 5 publications found

Genes affected

ENSG00000290067 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378005	XR_001744344.2	n.181-313G>A		intron_variant	Intron 2 of 4
LOC105378005	XR_007059769.1	n.432-313G>A		intron_variant	Intron 1 of 3
LOC105378005	XR_007059770.1	n.432-297G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290067	ENST00000702750.2	n.209-313G>A		intron_variant	Intron 2 of 4
ENSG00000290067	ENST00000771190.1	n.198-313G>A		intron_variant	Intron 2 of 4
ENSG00000290067	ENST00000771191.1	n.188-297G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63513 AN: 151842 Hom.: 18217 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.419 AC: 63633 AN: 151960 Hom.: 18272 Cov.: 31 AF XY: 0.409 AC XY: 30376 AN XY: 74258

African (AFR) AF: 0.816 AC: 33819 AN: 41470

American (AMR) AF: 0.338 AC: 5162 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3468

East Asian (EAS) AF: 0.142 AC: 733 AN: 5154

South Asian (SAS) AF: 0.148 AC: 710 AN: 4802

European-Finnish (FIN) AF: 0.221 AC: 2333 AN: 10558

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18568 AN: 67932

Other (OTH) AF: 0.427 AC: 900 AN: 2106

Alfa AF: 0.323 Hom.: 28818

Bravo AF: 0.451

Asia WGS AF: 0.202 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2078265; hg19: chr6-131761677;