18-57492696-T-C

Variant names:

• chr18-57492696-T-C
• rs3899444

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 0.554 in 152,032 control chromosomes in the GnomAD database, including 25,326 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 0.55 (25326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84277 AN: 151914 Hom.: 25322 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.554 AC: 84292 AN: 152032 Hom.: 25326 Cov.: 32 AF XY: 0.549 AC XY: 40761 AN XY: 74300

African (AFR) AF: 0.321 AC: 13314 AN: 41458

American (AMR) AF: 0.507 AC: 7750 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2464 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2684 AN: 5162

South Asian (SAS) AF: 0.593 AC: 2856 AN: 4814

European-Finnish (FIN) AF: 0.608 AC: 6419 AN: 10564

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46824 AN: 67972

Other (OTH) AF: 0.567 AC: 1196 AN: 2110

Alfa AF: 0.595 Hom.: 3701

Bravo AF: 0.533

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.7
DANN	Benign	0.87
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs3899444; hg19: chr18-55159928;