rs2728504

Variant names:

• chr18-25636846-G-A
• rs2728504

Your query was ambiguous. Multiple possible variants found:

• chr18-25636846-G-A
• chr18-25636846-G-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 0.337 in 151,812 control chromosomes in the GnomAD database, including 9,275 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 0.34 (9275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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: 0.337 AC: 51128 AN: 151694 Hom.: 9268 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.337 AC: 51154 AN: 151812 Hom.: 9275 Cov.: 32 AF XY: 0.345 AC XY: 25589 AN XY: 74196

African (AFR) AF: 0.231 AC: 9580 AN: 41432

American (AMR) AF: 0.407 AC: 6208 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3466

East Asian (EAS) AF: 0.314 AC: 1614 AN: 5132

South Asian (SAS) AF: 0.485 AC: 2326 AN: 4796

European-Finnish (FIN) AF: 0.478 AC: 5045 AN: 10556

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24583 AN: 67876

Other (OTH) AF: 0.335 AC: 706 AN: 2110

Alfa AF: 0.359 Hom.: 1791

Bravo AF: 0.324

Asia WGS AF: 0.409 AC: 1425 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	0.61
DANN	Benign	0.69
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs2728504; hg19: chr18-23216810;