18-53784243-G-C

Variant names:

• chr18-53784243-G-C
• rs10502984

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0284 in 152,284 control chromosomes in the GnomAD database, including 94 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 0.028 (94 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0284 (4320/152284) while in subpopulation AFR AF = 0.0513 (2131/41560). AF 95% confidence interval is 0.0495. There are 94 homozygotes in GnomAd4. There are 2038 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 94 gene

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: 0.0284 AC: 4314 AN: 152166 Hom.: 94 Cov.: 33

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0284 AC: 4320 AN: 152284 Hom.: 94 Cov.: 33 AF XY: 0.0274 AC XY: 2038 AN XY: 74462

African (AFR) AF: 0.0513 AC: 2131 AN: 41560

American (AMR) AF: 0.0230 AC: 351 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3472

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5190

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4826

European-Finnish (FIN) AF: 0.0135 AC: 143 AN: 10612

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0192 AC: 1303 AN: 68018

Other (OTH) AF: 0.0331 AC: 70 AN: 2116

Alfa AF: 0.0225 Hom.: 6

Bravo AF: 0.0300

Asia WGS AF: 0.0220 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10502984; hg19: chr18-51310613;