rs932026

chr18-38425547-G-A

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 0.137 in 152,100 control chromosomes in the GnomAD database, including 1,852 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 0.14 (1852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

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 (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.137 AC: 20888 AN: 151982 Hom.: 1849 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.137 AC: 20910 AN: 152100 Hom.: 1852 Cov.: 32 AF XY: 0.134 AC XY: 9987 AN XY: 74358

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.0337

Gnomad4 NFE AF: 0.0873

Gnomad4 OTH AF: 0.148

Alfa AF: 0.102 Hom.: 1246

Bravo AF: 0.148

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
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: rs932026; hg19: chr18-36005511;