18-5071786-T-C

Variant names:

• chr18-5071786-T-C
• rs188357

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 0.262 in 152,114 control chromosomes in the GnomAD database, including 5,274 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 (5274 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 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: 0.262 AC: 39832 AN: 151996 Hom.: 5264 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.262 AC: 39866 AN: 152114 Hom.: 5274 Cov.: 33 AF XY: 0.262 AC XY: 19494 AN XY: 74354

African (AFR) AF: 0.297 AC: 12306 AN: 41492

American (AMR) AF: 0.206 AC: 3155 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3464

East Asian (EAS) AF: 0.203 AC: 1048 AN: 5172

South Asian (SAS) AF: 0.342 AC: 1650 AN: 4818

European-Finnish (FIN) AF: 0.230 AC: 2429 AN: 10578

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17842 AN: 67978

Other (OTH) AF: 0.254 AC: 536 AN: 2114

Alfa AF: 0.258 Hom.: 8042

Bravo AF: 0.258

Asia WGS AF: 0.259 AC: 900 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	0.38
DANN	Benign	0.51
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs188357; hg19: chr18-5071785;