rs850889

Positions:

• chr2-185343521-C-T

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 0.517 in 151,826 control chromosomes in the GnomAD database, including 20,411 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 (20411 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.521 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: 0.517 AC: 78400 AN: 151708 Hom.: 20376 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.517 AC: 78482 AN: 151826 Hom.: 20411 Cov.: 32 AF XY: 0.520 AC XY: 38550 AN XY: 74160

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.517

Alfa AF: 0.521 Hom.: 3899

Bravo AF: 0.513

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs850889; hg19: chr2-186208248;