2-137867784-C-T

Variant names:

• chr2-137867784-C-T
• rs10460245
• ENST00000757541.1:n.150+2879G>A

Variant summary

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

The ENST00000757541.1(ENSG00000298715):​n.150+2879G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,100 control chromosomes in the GnomAD database, including 12,065 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 0.39 (12065 hom., cov: 31)
• Consequence: ENSG00000298715 ENST00000757541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 2 publications found

Genes affected

ENSG00000298715 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757541.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298715	ENST00000757541.1		n.150+2879G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58516 AN: 150984 Hom.: 12070 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.387 AC: 58500 AN: 151100 Hom.: 12065 Cov.: 31 AF XY: 0.391 AC XY: 28880 AN XY: 73790

African (AFR) AF: 0.256 AC: 10578 AN: 41328

American (AMR) AF: 0.373 AC: 5634 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2024 AN: 3450

East Asian (EAS) AF: 0.654 AC: 3354 AN: 5126

South Asian (SAS) AF: 0.553 AC: 2660 AN: 4814

European-Finnish (FIN) AF: 0.373 AC: 3926 AN: 10532

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 28918 AN: 67432

Other (OTH) AF: 0.434 AC: 909 AN: 2096

Alfa AF: 0.388 Hom.: 2088

Bravo AF: 0.377

Asia WGS AF: 0.542 AC: 1878 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.54
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10460245; hg19: chr2-138625354;