rs2617950

Positions:

• chr18-27729450-A-G

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 0.172 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.0946

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.0851

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.0886

Gnomad4 OTH AF: 0.144

Alfa AF: 0.101 Hom.: 1396

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2617950; hg19: chr18-25309414;