rs551556

Variant names:

• chr18-56584853-A-C
• rs551556

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 0.141 in 152,016 control chromosomes in the GnomAD database, including 1,639 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 0.14 (1639 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 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: 0.141 AC: 21354 AN: 151898 Hom.: 1631 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.141 AC: 21386 AN: 152016 Hom.: 1639 Cov.: 33 AF XY: 0.136 AC XY: 10141 AN XY: 74298

African (AFR) AF: 0.186 AC: 7705 AN: 41502

American (AMR) AF: 0.0955 AC: 1459 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 546 AN: 3460

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5188

South Asian (SAS) AF: 0.0881 AC: 425 AN: 4822

European-Finnish (FIN) AF: 0.118 AC: 1243 AN: 10576

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9593 AN: 67872

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.148 Hom.: 204

Bravo AF: 0.143

Asia WGS AF: 0.0410 AC: 143 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.93
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs551556; hg19: chr18-54252084;