rs1879352

Positions:

• chr18-2498055-T-C
• chr18-2498055-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;