chr2-184362344-C-T

Variant names:

• chr2-184362344-C-T
• rs1443022
• ENST00000671393.1:n.550-17814C>T

Variant summary

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

The ENST00000671393.1(ENSG00000286980):​n.550-17814C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,868 control chromosomes in the GnomAD database, including 19,909 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 (19909 hom., cov: 32)
• Consequence: ENSG00000286980 ENST00000671393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 0 publications found

Genes affected

ENSG00000286980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671393.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286980	ENST00000671393.1		n.550-17814C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73918 AN: 151748 Hom.: 19891 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.487 AC: 73957 AN: 151868 Hom.: 19909 Cov.: 32 AF XY: 0.494 AC XY: 36680 AN XY: 74232

African (AFR) AF: 0.266 AC: 11042 AN: 41452

American (AMR) AF: 0.585 AC: 8912 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3468

East Asian (EAS) AF: 0.896 AC: 4612 AN: 5150

South Asian (SAS) AF: 0.603 AC: 2911 AN: 4824

European-Finnish (FIN) AF: 0.622 AC: 6559 AN: 10540

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36625 AN: 67886

Other (OTH) AF: 0.493 AC: 1041 AN: 2112

Alfa AF: 0.527 Hom.: 33605

Bravo AF: 0.478

Asia WGS AF: 0.717 AC: 2488 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.094
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1443022;

hg19: chr2-185227071;