rs10485496

Variant names:

• chr20-6128102-T-C
• rs10485496

Your query was ambiguous. Multiple possible variants found:

• chr20-6128102-T-C
• chr20-6128102-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0767 in 152,240 control chromosomes in the GnomAD database, including 590 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 0.077 (590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11674 AN: 152122 Hom.: 589 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0767 AC: 11679 AN: 152240 Hom.: 590 Cov.: 32 AF XY: 0.0759 AC XY: 5651 AN XY: 74444

African (AFR) AF: 0.128 AC: 5327 AN: 41508

American (AMR) AF: 0.0556 AC: 851 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.110 AC: 529 AN: 4816

European-Finnish (FIN) AF: 0.0425 AC: 451 AN: 10616

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0598 AC: 4068 AN: 68030

Other (OTH) AF: 0.0696 AC: 147 AN: 2112

Alfa AF: 0.0547 Hom.: 131

Bravo AF: 0.0781

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.3
DANN	Benign	0.84
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10485496; hg19: chr20-6108749;