2-134107625-T-C

Variant names:

• chr2-134107625-T-C
• rs1996589
• ENST00000760060.1:n.1248A>G

Variant summary

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

The ENST00000760060.1(ENSG00000299039):​n.1248A>G 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 0.383 in 151,984 control chromosomes in the GnomAD database, including 12,855 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 0.38 (12855 hom., cov: 32)
• Consequence: ENSG00000299039 ENST00000760060.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 3 publications found

Genes affected

ENSG00000299039 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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
ENSG00000299039	ENST00000760060.1	n.1248A>G		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58107 AN: 151866 Hom.: 12814 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.383 AC: 58200 AN: 151984 Hom.: 12855 Cov.: 32 AF XY: 0.376 AC XY: 27968 AN XY: 74304

African (AFR) AF: 0.615 AC: 25485 AN: 41416

American (AMR) AF: 0.297 AC: 4534 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1327 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2130 AN: 5168

South Asian (SAS) AF: 0.307 AC: 1477 AN: 4814

European-Finnish (FIN) AF: 0.193 AC: 2037 AN: 10580

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19945 AN: 67954

Other (OTH) AF: 0.420 AC: 885 AN: 2108

Alfa AF: 0.354 Hom.: 15445

Bravo AF: 0.403

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.60
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1996589; hg19: chr2-134865196; COSMIC: COSV67072169;