rs1504116

Variant names:

• chr18-28539096-A-G
• rs1504116

Your query was ambiguous. Multiple possible variants found:

• chr18-28539096-A-G
• chr18-28539096-A-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 0.256 in 152,124 control chromosomes in the GnomAD database, including 5,214 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 0.26 (5214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 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: 0.256 AC: 38947 AN: 152006 Hom.: 5213 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.256 AC: 38955 AN: 152124 Hom.: 5214 Cov.: 32 AF XY: 0.255 AC XY: 18987 AN XY: 74374

African (AFR) AF: 0.250 AC: 10389 AN: 41490

American (AMR) AF: 0.236 AC: 3606 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 668 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1100 AN: 5164

South Asian (SAS) AF: 0.261 AC: 1256 AN: 4816

European-Finnish (FIN) AF: 0.245 AC: 2594 AN: 10588

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18654 AN: 67982

Other (OTH) AF: 0.243 AC: 513 AN: 2112

Alfa AF: 0.148 Hom.: 281

Bravo AF: 0.253

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.70
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1504116; hg19: chr18-26119060;