rs56387543

Positions:

• chr20-45173959-GT-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.154 in 149,250 control chromosomes in the GnomAD database, including 1,876 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1876 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.154 AC: 22983 AN: 149118 Hom.: 1871 Cov.: 28

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.154 AC: 23022 AN: 149250 Hom.: 1876 Cov.: 28 AF XY: 0.155 AC XY: 11298 AN XY: 72880

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0378

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.168

Alfa AF: 0.165 Hom.: 249

Bravo AF: 0.146

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56387543; hg19: chr20-43802600;