ENST00000739907.1:n.115-265C>T

Variant names:

• chr2-36167970-C-T
• rs1167465
• ENST00000739907.1:n.115-265C>T

Variant summary

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

The ENST00000739907.1(ENSG00000296492):​n.115-265C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,022 control chromosomes in the GnomAD database, including 28,972 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 0.61 (28972 hom., cov: 32)
• Consequence: ENSG00000296492 ENST00000739907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 3 publications found

Genes affected

ENSG00000296492 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 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
ENSG00000296492	ENST00000739907.1	n.115-265C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93332 AN: 151904 Hom.: 28946 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.614 AC: 93412 AN: 152022 Hom.: 28972 Cov.: 32 AF XY: 0.610 AC XY: 45355 AN XY: 74312

African (AFR) AF: 0.639 AC: 26493 AN: 41450

American (AMR) AF: 0.581 AC: 8866 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1852 AN: 3466

East Asian (EAS) AF: 0.838 AC: 4348 AN: 5188

South Asian (SAS) AF: 0.615 AC: 2957 AN: 4812

European-Finnish (FIN) AF: 0.543 AC: 5724 AN: 10548

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41098 AN: 67976

Other (OTH) AF: 0.628 AC: 1325 AN: 2110

Alfa AF: 0.607 Hom.: 6598

Bravo AF: 0.619

Asia WGS AF: 0.727 AC: 2515 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.098
DANN	Benign	0.59
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1167465; hg19: chr2-36395113;