rs2617950

Variant names:

• chr18-27729450-A-G
• rs2617950

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 0.172 in 152,086 control chromosomes in the GnomAD database, including 3,723 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 0.17 (3723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 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: 0.172 AC: 26098 AN: 151968 Hom.: 3710 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.0999

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.172 AC: 26155 AN: 152086 Hom.: 3723 Cov.: 32 AF XY: 0.168 AC XY: 12512 AN XY: 74352

African (AFR) AF: 0.393 AC: 16274 AN: 41444

American (AMR) AF: 0.0946 AC: 1446 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.100 AC: 516 AN: 5162

South Asian (SAS) AF: 0.0851 AC: 411 AN: 4828

European-Finnish (FIN) AF: 0.0758 AC: 804 AN: 10602

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0886 AC: 6021 AN: 67978

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.110 Hom.: 2267

Bravo AF: 0.185

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.67
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2617950; hg19: chr18-25309414;