2-115938858-C-T

Variant names:

• chr2-115938858-C-T
• rs1447241
• ENST00000668438.1:n.360+1074G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668438.1(ENSG00000287451):​n.360+1074G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,930 control chromosomes in the GnomAD database, including 19,897 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 0.49 (19897 hom., cov: 32)
• Consequence: ENSG00000287451 ENST00000668438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

Genes affected

ENSG00000287451 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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
ENSG00000287451	ENST00000668438.1	n.360+1074G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74089 AN: 151814 Hom.: 19868 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.488 AC: 74169 AN: 151930 Hom.: 19897 Cov.: 32 AF XY: 0.486 AC XY: 36062 AN XY: 74226

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.464

Alfa AF: 0.418 Hom.: 9139

Bravo AF: 0.510

Asia WGS AF: 0.624 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1447241; hg19: chr2-116696434;