18-49767489-T-C

Variant names:

• chr18-49767489-T-C
• rs1790480

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 0.605 in 151,936 control chromosomes in the GnomAD database, including 27,887 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 0.60 (27887 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91774 AN: 151818 Hom.: 27868 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.605 AC: 91846 AN: 151936 Hom.: 27887 Cov.: 31 AF XY: 0.604 AC XY: 44853 AN XY: 74234

African (AFR) AF: 0.620 AC: 25685 AN: 41420

American (AMR) AF: 0.647 AC: 9887 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2430 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2821 AN: 5150

South Asian (SAS) AF: 0.586 AC: 2821 AN: 4816

European-Finnish (FIN) AF: 0.528 AC: 5568 AN: 10538

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40399 AN: 67954

Other (OTH) AF: 0.643 AC: 1359 AN: 2112

Alfa AF: 0.461 Hom.: 1148

Bravo AF: 0.618

Asia WGS AF: 0.592 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.78
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1790480; hg19: chr18-47293859;