chr2-49487883-G-A

Variant names:

• chr2-49487883-G-A
• rs12987465
• ENST00000753905.1:n.242-33023C>T

Variant summary

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

The ENST00000753905.1(ENSG00000282998):​n.242-33023C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,718 control chromosomes in the GnomAD database, including 13,324 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 0.41 (13324 hom., cov: 31)
• Consequence: ENSG00000282998 ENST00000753905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 5 publications found

Genes affected

ENSG00000282998 (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 (AFR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753905.1. 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
	ENSG00000282998	ENST00000753905.1		n.242-33023C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61755 AN: 151600 Hom.: 13311 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.407 AC: 61790 AN: 151718 Hom.: 13324 Cov.: 31 AF XY: 0.410 AC XY: 30410 AN XY: 74136

African (AFR) AF: 0.537 AC: 22205 AN: 41370

American (AMR) AF: 0.447 AC: 6803 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3466

East Asian (EAS) AF: 0.521 AC: 2684 AN: 5156

South Asian (SAS) AF: 0.391 AC: 1880 AN: 4808

European-Finnish (FIN) AF: 0.353 AC: 3700 AN: 10484

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22092 AN: 67890

Other (OTH) AF: 0.404 AC: 854 AN: 2112

Alfa AF: 0.352 Hom.: 45452

Bravo AF: 0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.34
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12987465; hg19: chr2-49715021;