rs1646807

Positions:

• chr18-53861827-T-A
• chr18-53861827-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 0.78 in 152,062 control chromosomes in the GnomAD database, including 46,783 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 0.78 (46783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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: 0.780 AC: 118486 AN: 151944 Hom.: 46745 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.780 AC: 118581 AN: 152062 Hom.: 46783 Cov.: 31 AF XY: 0.783 AC XY: 58186 AN XY: 74344

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.818

Alfa AF: 0.799 Hom.: 6060

Bravo AF: 0.779

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1646807; hg19: chr18-51388197;