rs2851757

Variant names:

• chr18-27733137-C-T
• rs2851757

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 0.123 in 151,792 control chromosomes in the GnomAD database, including 1,454 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 0.12 (1454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.930
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18702 AN: 151676 Hom.: 1455 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0850

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.123 AC: 18713 AN: 151792 Hom.: 1454 Cov.: 32 AF XY: 0.121 AC XY: 9012 AN XY: 74186

African (AFR) AF: 0.226 AC: 9361 AN: 41350

American (AMR) AF: 0.0740 AC: 1129 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3470

East Asian (EAS) AF: 0.103 AC: 532 AN: 5142

South Asian (SAS) AF: 0.0847 AC: 408 AN: 4818

European-Finnish (FIN) AF: 0.0767 AC: 807 AN: 10526

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5901 AN: 67926

Other (OTH) AF: 0.108 AC: 228 AN: 2106

Alfa AF: 0.0963 Hom.: 3353

Bravo AF: 0.128

Asia WGS AF: 0.102 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.70
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs2851757; hg19: chr18-25313101;