rs10485751

Variant names:

• chr20-11998547-C-T
• rs10485751

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 0.0513 in 152,062 control chromosomes in the GnomAD database, including 440 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 0.051 (440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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: 0.0512 AC: 7780 AN: 151944 Hom.: 437 Cov.: 32

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.00377

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0513 AC: 7795 AN: 152062 Hom.: 440 Cov.: 32 AF XY: 0.0547 AC XY: 4069 AN XY: 74334

Gnomad4 AFR AF: 0.0777

Gnomad4 AMR AF: 0.0920

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.00377

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0270 Hom.: 295

Bravo AF: 0.0567

Asia WGS AF: 0.159 AC: 552 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	3.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485751; hg19: chr20-11979195;