rs1039189

Positions:

• chr18-53951084-A-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 0.176 in 152,078 control chromosomes in the GnomAD database, including 2,647 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 0.18 (2647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 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: 0.176 AC: 26802 AN: 151958 Hom.: 2647 Cov.: 32

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.176 AC: 26803 AN: 152078 Hom.: 2647 Cov.: 32 AF XY: 0.175 AC XY: 13030 AN XY: 74330

Gnomad4 AFR AF: 0.0966

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0499

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.164

Alfa AF: 0.204 Hom.: 383

Bravo AF: 0.166

Asia WGS AF: 0.117 AC: 407 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1039189; hg19: chr18-51477454;