rs1229587

Variant names:

• chr18-56240105-G-A
• rs1229587

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 152,188 control chromosomes in the GnomAD database, including 46,684 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 (46684 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 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: 0.780 AC: 118559 AN: 152070 Hom.: 46632 Cov.: 33

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.780 AC: 118672 AN: 152188 Hom.: 46684 Cov.: 33 AF XY: 0.780 AC XY: 57986 AN XY: 74386

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.774

Alfa AF: 0.759 Hom.: 6934

Bravo AF: 0.789

Asia WGS AF: 0.848 AC: 2948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1229587; hg19: chr18-53907336;