rs4810544

Positions:

• chr20-46706399-T-C
• chr20-46706399-T-G

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 0.162 in 152,134 control chromosomes in the GnomAD database, including 2,486 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 0.16 (2486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24522 AN: 152016 Hom.: 2460 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.162 AC: 24599 AN: 152134 Hom.: 2486 Cov.: 32 AF XY: 0.165 AC XY: 12281 AN XY: 74370

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.142

Alfa AF: 0.112 Hom.: 225

Bravo AF: 0.169

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4810544; hg19: chr20-45335038;