rs4939883

Positions:

• chr18-49640844-T-C
• chr18-49640844-T-G

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 0.754 in 152,102 control chromosomes in the GnomAD database, including 44,641 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 0.75 (44641 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.49640844T>C		intergenic_region
LOC105372112	XR_007066363.1	n.179-21190T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114612 AN: 151984 Hom.: 44618 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.754 AC: 114675 AN: 152102 Hom.: 44641 Cov.: 32 AF XY: 0.760 AC XY: 56508 AN XY: 74378

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.778

Alfa AF: 0.825 Hom.: 80466

Bravo AF: 0.747

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939883; hg19: chr18-47167214;