18-56267556-A-G

Variant names:

• chr18-56267556-A-G
• rs1229598

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 0.785 in 152,030 control chromosomes in the GnomAD database, including 47,482 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 0.79 (47482 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 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: 0.785 AC: 119225 AN: 151912 Hom.: 47421 Cov.: 31

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.785 AC: 119350 AN: 152030 Hom.: 47482 Cov.: 31 AF XY: 0.783 AC XY: 58198 AN XY: 74286

African (AFR) AF: 0.909 AC: 37725 AN: 41518

American (AMR) AF: 0.785 AC: 11999 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2616 AN: 3468

East Asian (EAS) AF: 0.929 AC: 4797 AN: 5164

South Asian (SAS) AF: 0.643 AC: 3090 AN: 4806

European-Finnish (FIN) AF: 0.701 AC: 7373 AN: 10512

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49236 AN: 67968

Other (OTH) AF: 0.779 AC: 1643 AN: 2110

Alfa AF: 0.747 Hom.: 10514

Bravo AF: 0.799

Asia WGS AF: 0.797 AC: 2772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1229598; hg19: chr18-53934787;