2-184362344-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373776	XR_001739817.2	n.63-1951G>A		intron_variant	Intron 1 of 4
LOC102724340	XR_001739819.1	n.318+29451C>T		intron_variant	Intron 3 of 4
LOC105373776	XR_923647.3	n.133-1951G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286980	ENST00000671393.1	n.550-17814C>T		intron_variant	Intron 4 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs1443022; hg19: chr2-185227071;