rs1561234

Variant names:

• chr18-54444819-A-G
• rs1561234

Your query was ambiguous. Multiple possible variants found:

• chr18-54444819-A-G
• chr18-54444819-A-T

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 0.417 in 151,986 control chromosomes in the GnomAD database, including 15,694 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 0.42 (15694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.418 AC: 63415 AN: 151868 Hom.: 15695 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.417 AC: 63421 AN: 151986 Hom.: 15694 Cov.: 32 AF XY: 0.425 AC XY: 31542 AN XY: 74300

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.477

Alfa AF: 0.483 Hom.: 12224

Bravo AF: 0.411

Asia WGS AF: 0.528 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561234; hg19: chr18-51971189;