rs2217945

Variant names:

• chr18-40605094-C-T
• rs2217945

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 0.36 in 151,958 control chromosomes in the GnomAD database, including 10,888 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 0.36 (10888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.360 AC: 54687 AN: 151840 Hom.: 10882 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.360 AC: 54720 AN: 151958 Hom.: 10888 Cov.: 32 AF XY: 0.371 AC XY: 27580 AN XY: 74258

African (AFR) AF: 0.233 AC: 9650 AN: 41452

American (AMR) AF: 0.436 AC: 6647 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3823 AN: 5174

South Asian (SAS) AF: 0.624 AC: 3008 AN: 4818

European-Finnish (FIN) AF: 0.398 AC: 4187 AN: 10528

Middle Eastern (MID) AF: 0.376 AC: 109 AN: 290

European-Non Finnish (NFE) AF: 0.368 AC: 24979 AN: 67952

Other (OTH) AF: 0.372 AC: 785 AN: 2110

Alfa AF: 0.342 Hom.: 1212

Bravo AF: 0.354

Asia WGS AF: 0.699 AC: 2430 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.25
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2217945; hg19: chr18-38185058;