rs17784795

chr18-47202373-T-C

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 0.102 in 152,240 control chromosomes in the GnomAD database, including 836 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 0.10 (836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 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: 0.102 AC: 15510 AN: 152120 Hom.: 833 Cov.: 32

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.0913

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0961

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

GnomAD4 genome AF: 0.102 AC: 15545 AN: 152240 Hom.: 836 Cov.: 32 AF XY: 0.101 AC XY: 7507 AN XY: 74442

Gnomad4 AFR AF: 0.0851

Gnomad4 AMR AF: 0.0804

Gnomad4 ASJ AF: 0.0913

Gnomad4 EAS AF: 0.0985

Gnomad4 SAS AF: 0.0483

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.109 Hom.: 320

Bravo AF: 0.0972

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.4
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17784795; hg19: chr18-44728744;