chr2-200244264-C-A

Variant names:

• chr2-200244264-C-A
• rs1369842
• ENST00000750357.1:n.270+14671G>T

Variant summary

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

The ENST00000750357.1(ENSG00000297701):​n.270+14671G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,608 control chromosomes in the GnomAD database, including 21,551 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 0.52 (21551 hom., cov: 30)
• Consequence: ENSG00000297701 ENST00000750357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 7 publications found

Genes affected

ENSG00000297701 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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
ENSG00000297701	ENST00000750357.1	n.270+14671G>T		intron_variant	Intron 1 of 2
ENSG00000297701	ENST00000750358.1	n.112+14671G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79206 AN: 151490 Hom.: 21524 Cov.: 30

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.523 AC: 79278 AN: 151608 Hom.: 21551 Cov.: 30 AF XY: 0.531 AC XY: 39321 AN XY: 74082

African (AFR) AF: 0.374 AC: 15423 AN: 41276

American (AMR) AF: 0.627 AC: 9542 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1702 AN: 3468

East Asian (EAS) AF: 0.766 AC: 3944 AN: 5146

South Asian (SAS) AF: 0.587 AC: 2793 AN: 4762

European-Finnish (FIN) AF: 0.634 AC: 6665 AN: 10510

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37563 AN: 67908

Other (OTH) AF: 0.525 AC: 1107 AN: 2108

Alfa AF: 0.535 Hom.: 2754

Bravo AF: 0.518

Asia WGS AF: 0.674 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.18
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1369842; hg19: chr2-201108987;