2-127129099-C-T

Variant names:

• chr2-127129099-C-T
• rs13031703
• ENST00000726607.1:n.342-6161C>T

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-6161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,210 control chromosomes in the GnomAD database, including 1,168 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 0.12 (1168 hom., cov: 33)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 10 publications found

Genes affected

ENSG00000294899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373605	XR_923310.3	n.449-4139C>T		intron_variant	Intron 2 of 3
LOC105373605	XR_923311.4	n.846-4139C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294899	ENST00000726607.1	n.342-6161C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17759 AN: 152092 Hom.: 1169 Cov.: 33

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.117 AC: 17761 AN: 152210 Hom.: 1168 Cov.: 33 AF XY: 0.120 AC XY: 8896 AN XY: 74412

African (AFR) AF: 0.0683 AC: 2839 AN: 41548

American (AMR) AF: 0.105 AC: 1603 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0854 AC: 296 AN: 3468

East Asian (EAS) AF: 0.113 AC: 588 AN: 5188

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4818

European-Finnish (FIN) AF: 0.160 AC: 1693 AN: 10572

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9168 AN: 68006

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.130 Hom.: 1808

Bravo AF: 0.105

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.72
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs13031703; hg19: chr2-127886675;