rs12955983

Variant names:

• chr18-60205756-A-G
• rs12955983

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 152,100 control chromosomes in the GnomAD database, including 3,607 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 (3607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 20 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 (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: 0.203 AC: 30783 AN: 151982 Hom.: 3605 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.264

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: 30784 AN: 152100 Hom.: 3607 Cov.: 32 AF XY: 0.199 AC XY: 14810 AN XY: 74348

African (AFR) AF: 0.102 AC: 4253 AN: 41534

American (AMR) AF: 0.167 AC: 2545 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3470

East Asian (EAS) AF: 0.169 AC: 872 AN: 5162

South Asian (SAS) AF: 0.343 AC: 1651 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1933 AN: 10574

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17943 AN: 67956

Other (OTH) AF: 0.212 AC: 449 AN: 2116

Alfa AF: 0.216 Hom.: 1490

Bravo AF: 0.196

Asia WGS AF: 0.203 AC: 707 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	1.8
DANN	Benign	0.86
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs12955983; hg19: chr18-57872989;