18-49767489-T-C

Variant names:

• chr18-49767489-T-C
• rs1790480

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 0.605 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

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 (AMR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.643

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1790480; hg19: chr18-47293859;