rs10485682

chr20-41890348-C-T

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 0.0195 in 151,974 control chromosomes in the GnomAD database, including 138 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 0.020 (138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 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: 0.0195 AC: 2965 AN: 151858 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.00538

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.00464

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00459

Gnomad OTH AF: 0.0317

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

GnomAD4 genome AF: 0.0195 AC: 2964 AN: 151974 Hom.: 138 Cov.: 32 AF XY: 0.0208 AC XY: 1546 AN XY: 74276

Gnomad4 AFR AF: 0.00536

Gnomad4 AMR AF: 0.0958

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.00464

Gnomad4 NFE AF: 0.00459

Gnomad4 OTH AF: 0.0304

Alfa AF: 0.00984 Hom.: 43

Bravo AF: 0.0308

Asia WGS AF: 0.0660 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485682; hg19: chr20-40518988;