rs1369842

Positions:

• chr2-200244264-C-A
• chr2-200244264-C-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;