rs4939875

Positions:

• chr18-49555944-G-C

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 0.826 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.846

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939875; hg19: chr18-47082314;