rs870504

Positions:

• chr18-28350665-C-A
• chr18-28350665-C-T

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 0.362 in 151,894 control chromosomes in the GnomAD database, including 10,984 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 0.36 (10984 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54926 AN: 151776 Hom.: 10984 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.362 AC: 54938 AN: 151894 Hom.: 10984 Cov.: 32 AF XY: 0.361 AC XY: 26823 AN XY: 74204

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.430

Alfa AF: 0.391 Hom.: 6242

Bravo AF: 0.357

Asia WGS AF: 0.359 AC: 1248 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.4
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs870504; hg19: chr18-25930629;