chr18-42149837-T-C

Variant names:

• chr18-42149837-T-C
• rs673154

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 0.758 in 151,324 control chromosomes in the GnomAD database, including 44,421 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 0.76 (44421 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.808 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: 0.759 AC: 114692 AN: 151204 Hom.: 44419 Cov.: 30

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.758 AC: 114724 AN: 151324 Hom.: 44421 Cov.: 30 AF XY: 0.762 AC XY: 56317 AN XY: 73946

African (AFR) AF: 0.595 AC: 24517 AN: 41214

American (AMR) AF: 0.818 AC: 12446 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2683 AN: 3456

East Asian (EAS) AF: 0.817 AC: 4180 AN: 5116

South Asian (SAS) AF: 0.809 AC: 3884 AN: 4800

European-Finnish (FIN) AF: 0.889 AC: 9349 AN: 10514

Middle Eastern (MID) AF: 0.825 AC: 236 AN: 286

European-Non Finnish (NFE) AF: 0.813 AC: 55079 AN: 67722

Other (OTH) AF: 0.770 AC: 1615 AN: 2098

Alfa AF: 0.794 Hom.: 5886

Bravo AF: 0.745

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.87
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs673154; hg19: chr18-39729801;