rs2048135

Variant names:

• chr18-76031433-G-A
• rs2048135

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.203 AC: 8427 AN: 41444

American (AMR) AF: 0.292 AC: 4457 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3468

East Asian (EAS) AF: 0.0485 AC: 251 AN: 5174

South Asian (SAS) AF: 0.105 AC: 505 AN: 4812

European-Finnish (FIN) AF: 0.321 AC: 3387 AN: 10552

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17908 AN: 67926

Other (OTH) AF: 0.244 AC: 514 AN: 2108

Alfa AF: 0.238 Hom.: 4011

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2048135; hg19: chr18-73743388;