rs870504

Variant names:

• chr18-28350665-C-A
• rs870504

Your query was ambiguous. Multiple possible variants found:

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

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 0.362 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.191 AC: 7901 AN: 41446

American (AMR) AF: 0.391 AC: 5962 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2127 AN: 5124

South Asian (SAS) AF: 0.359 AC: 1730 AN: 4824

European-Finnish (FIN) AF: 0.395 AC: 4164 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29658 AN: 67920

Other (OTH) AF: 0.430 AC: 906 AN: 2106

Alfa AF: 0.396 Hom.: 9161

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs870504; hg19: chr18-25930629;