rs10485803

Positions:

• chr20-55957834-T-C

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 0.0678 in 152,192 control chromosomes in the GnomAD database, including 416 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 0.068 (416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0785 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: 0.0678 AC: 10313 AN: 152074 Hom.: 416 Cov.: 31

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0694

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0678 AC: 10324 AN: 152192 Hom.: 416 Cov.: 31 AF XY: 0.0700 AC XY: 5207 AN XY: 74424

Gnomad4 AFR AF: 0.0394

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0700

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.0738

Alfa AF: 0.0818 Hom.: 692

Bravo AF: 0.0624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485803; hg19: chr20-54532890;