ENST00000762706.1:n.405-33267C>T

Variant names:

• chr2-112851991-C-T
• rs13008855
• ENST00000762706.1:n.405-33267C>T

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.405-33267C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,022 control chromosomes in the GnomAD database, including 5,282 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 0.23 (5282 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 12 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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
ENSG00000299339	ENST00000762706.1	n.405-33267C>T		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.500-33267C>T		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.266-33267C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35590 AN: 151904 Hom.: 5263 Cov.: 31

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.234 AC: 35626 AN: 152022 Hom.: 5282 Cov.: 31 AF XY: 0.244 AC XY: 18117 AN XY: 74282

African (AFR) AF: 0.0653 AC: 2711 AN: 41530

American (AMR) AF: 0.395 AC: 6038 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2145 AN: 5172

South Asian (SAS) AF: 0.357 AC: 1715 AN: 4798

European-Finnish (FIN) AF: 0.334 AC: 3514 AN: 10532

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18068 AN: 67940

Other (OTH) AF: 0.243 AC: 513 AN: 2108

Alfa AF: 0.263 Hom.: 1000

Bravo AF: 0.231

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.1
DANN	Benign	0.78
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs13008855; hg19: chr2-113609568; COSMIC: COSV57239633;