2-200244264-C-A

Variant names:

• chr2-200244264-C-A
• rs1369842

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.525

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369842; hg19: chr2-201108987;