rs1942872

Variant names:

• chr18-60201132-C-T
• rs1942872

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.213 in 151,774 control chromosomes in the GnomAD database, including 3,820 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 0.21 (3820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 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: 0.214 AC: 32392 AN: 151656 Hom.: 3818 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.213 AC: 32400 AN: 151774 Hom.: 3820 Cov.: 32 AF XY: 0.210 AC XY: 15559 AN XY: 74150

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.218

Alfa AF: 0.228 Hom.: 535

Bravo AF: 0.208

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1942872; hg19: chr18-57868365;