rs1942872

chr18-60201132-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;