rs2048135

Positions:

• chr18-76031433-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 0.241 in 151,956 control chromosomes in the GnomAD database, including 4,708 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 0.24 (4708 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.76031433G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36598 AN: 151838 Hom.: 4710 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.241 AC: 36598 AN: 151956 Hom.: 4708 Cov.: 32 AF XY: 0.242 AC XY: 17943 AN XY: 74266

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0485

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.244

Alfa AF: 0.247 Hom.: 2805

Bravo AF: 0.238

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048135; hg19: chr18-73743388;