rs2217945

chr18-40605094-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 0.36 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.372

Alfa AF: 0.347 Hom.: 1194

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2217945; hg19: chr18-38185058;