2-235216378-C-T

Variant names:

• chr2-235216378-C-T
• rs2060127
• ENST00000762435.1:n.127-12406G>A

Variant summary

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

The ENST00000762435.1(ENSG00000299301):​n.127-12406G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,090 control chromosomes in the GnomAD database, including 40,881 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 0.73 (40881 hom., cov: 32)
• Consequence: ENSG00000299301 ENST00000762435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 2 publications found

Genes affected

ENSG00000299301 (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 = 0.895 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
ENSG00000299301	ENST00000762435.1	n.127-12406G>A		intron_variant	Intron 1 of 2
ENSG00000299301	ENST00000762436.1	n.101+11265G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110462 AN: 151972 Hom.: 40840 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.727 AC: 110559 AN: 152090 Hom.: 40881 Cov.: 32 AF XY: 0.729 AC XY: 54178 AN XY: 74360

African (AFR) AF: 0.592 AC: 24552 AN: 41476

American (AMR) AF: 0.704 AC: 10763 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2659 AN: 3470

East Asian (EAS) AF: 0.917 AC: 4726 AN: 5154

South Asian (SAS) AF: 0.860 AC: 4146 AN: 4822

European-Finnish (FIN) AF: 0.778 AC: 8240 AN: 10596

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53067 AN: 67980

Other (OTH) AF: 0.740 AC: 1559 AN: 2106

Alfa AF: 0.739 Hom.: 7071

Bravo AF: 0.715

Asia WGS AF: 0.874 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.020
DANN	Benign	0.22
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2060127; hg19: chr2-236125022;