chr18-60236371-T-C

Variant names:

• chr18-60236371-T-C
• rs12964203

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 0.202 in 151,878 control chromosomes in the GnomAD database, including 3,572 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 0.20 (3572 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• 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: 0.202 AC: 30642 AN: 151762 Hom.: 3571 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.202 AC: 30643 AN: 151878 Hom.: 3572 Cov.: 31 AF XY: 0.199 AC XY: 14744 AN XY: 74242

African (AFR) AF: 0.103 AC: 4276 AN: 41484

American (AMR) AF: 0.167 AC: 2550 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3466

East Asian (EAS) AF: 0.176 AC: 910 AN: 5168

South Asian (SAS) AF: 0.342 AC: 1647 AN: 4812

European-Finnish (FIN) AF: 0.182 AC: 1929 AN: 10588

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.262 AC: 17753 AN: 67824

Other (OTH) AF: 0.212 AC: 447 AN: 2104

Alfa AF: 0.244 Hom.: 13448

Bravo AF: 0.196

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs12964203; hg19: chr18-57903604;