chr18-49555944-G-C

Variant names:

• chr18-49555944-G-C
• rs4939875

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 0.826 in 152,160 control chromosomes in the GnomAD database, including 52,894 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 0.83 (52894 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 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: 0.826 AC: 125644 AN: 152040 Hom.: 52843 Cov.: 33

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.826 AC: 125745 AN: 152160 Hom.: 52894 Cov.: 33 AF XY: 0.820 AC XY: 60997 AN XY: 74380

African (AFR) AF: 0.958 AC: 39830 AN: 41556

American (AMR) AF: 0.667 AC: 10192 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3043 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2872 AN: 5160

South Asian (SAS) AF: 0.826 AC: 3970 AN: 4806

European-Finnish (FIN) AF: 0.729 AC: 7701 AN: 10566

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55307 AN: 68012

Other (OTH) AF: 0.846 AC: 1788 AN: 2114

Alfa AF: 0.828 Hom.: 6574

Bravo AF: 0.824

Asia WGS AF: 0.725 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.37
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4939875; hg19: chr18-47082314;