18-2498055-T-C

Variant names:

• chr18-2498055-T-C
• rs1879352

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 0.112 in 152,252 control chromosomes in the GnomAD database, including 1,238 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 0.11 (1238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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: 0.112 AC: 17001 AN: 152134 Hom.: 1235 Cov.: 32

Gnomad AFR AF: 0.0424

Gnomad AMI AF: 0.0650

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0476

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.112 AC: 17007 AN: 152252 Hom.: 1238 Cov.: 32 AF XY: 0.109 AC XY: 8130 AN XY: 74438

Gnomad4 AFR AF: 0.0424

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0477

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0887

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.132

Alfa AF: 0.147 Hom.: 3305

Bravo AF: 0.112

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879352; hg19: chr18-2498054;