rs2850889

Variant names:

• chr18-77246651-T-C
• rs2850889

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 0.402 in 151,960 control chromosomes in the GnomAD database, including 12,662 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 0.40 (12662 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 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: 0.402 AC: 61111 AN: 151842 Hom.: 12651 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.402 AC: 61149 AN: 151960 Hom.: 12662 Cov.: 31 AF XY: 0.400 AC XY: 29693 AN XY: 74278

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.407

Alfa AF: 0.448 Hom.: 31537

Bravo AF: 0.395

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2850889; hg19: chr18-74958607;