rs850889

Variant names:

• chr2-185343521-C-T
• rs850889

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.517 AC: 21434 AN: 41456

American (AMR) AF: 0.530 AC: 8088 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1416 AN: 3462

East Asian (EAS) AF: 0.482 AC: 2477 AN: 5142

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4812

European-Finnish (FIN) AF: 0.611 AC: 6454 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35131 AN: 67830

Other (OTH) AF: 0.517 AC: 1090 AN: 2108

Alfa AF: 0.520 Hom.: 3983

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
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs850889; hg19: chr2-186208248;