2-115938858-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000287451 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668438.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287451	ENST00000668438.1		n.360+1074G>A		intron	N/A
	ENSG00000287451	ENST00000773149.1		n.119+1074G>A		intron	N/A
	ENSG00000287451	ENST00000773150.1		n.116+1074G>A		intron	N/A

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

African (AFR) AF: 0.702 AC: 29097 AN: 41442

American (AMR) AF: 0.405 AC: 6169 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1756 AN: 3466

East Asian (EAS) AF: 0.729 AC: 3746 AN: 5142

South Asian (SAS) AF: 0.493 AC: 2376 AN: 4820

European-Finnish (FIN) AF: 0.282 AC: 2973 AN: 10554

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26578 AN: 67948

Other (OTH) AF: 0.464 AC: 980 AN: 2110

Alfa AF: 0.431 Hom.: 14873

Bravo AF: 0.510

Asia WGS AF: 0.624 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.68
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1447241; hg19: chr2-116696434;