rs56191952

Variant names:

• chr20-45173846-A-G
• rs56191952

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 0.152 in 151,758 control chromosomes in the GnomAD database, including 1,863 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 0.15 (1863 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 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: 0.152 AC: 23024 AN: 151640 Hom.: 1858 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.152 AC: 23063 AN: 151758 Hom.: 1863 Cov.: 31 AF XY: 0.153 AC XY: 11326 AN XY: 74148

African (AFR) AF: 0.122 AC: 5042 AN: 41366

American (AMR) AF: 0.130 AC: 1978 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3466

East Asian (EAS) AF: 0.0348 AC: 180 AN: 5178

South Asian (SAS) AF: 0.144 AC: 691 AN: 4796

European-Finnish (FIN) AF: 0.188 AC: 1982 AN: 10532

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11768 AN: 67864

Other (OTH) AF: 0.167 AC: 352 AN: 2102

Alfa AF: 0.163 Hom.: 261

Bravo AF: 0.146

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.47
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs56191952; hg19: chr20-43802487;