chr18-43374722-T-C

Variant names:

• chr18-43374722-T-C
• rs679832

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 0.493 in 151,758 control chromosomes in the GnomAD database, including 21,581 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 0.49 (21581 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74658 AN: 151640 Hom.: 21539 Cov.: 30

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.493 AC: 74746 AN: 151758 Hom.: 21581 Cov.: 30 AF XY: 0.496 AC XY: 36783 AN XY: 74110

African (AFR) AF: 0.753 AC: 31141 AN: 41376

American (AMR) AF: 0.479 AC: 7296 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5052 AN: 5114

South Asian (SAS) AF: 0.454 AC: 2184 AN: 4806

European-Finnish (FIN) AF: 0.369 AC: 3880 AN: 10522

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22804 AN: 67922

Other (OTH) AF: 0.450 AC: 945 AN: 2100

Alfa AF: 0.414 Hom.: 2281

Bravo AF: 0.516

Asia WGS AF: 0.709 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.41
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs679832; hg19: chr18-40954687;