rs10485706

chr20-6868719-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 0.0946 in 152,230 control chromosomes in the GnomAD database, including 2,148 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 0.095 (2148 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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: 0.0941 AC: 14318 AN: 152112 Hom.: 2119 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00575

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0946 AC: 14395 AN: 152230 Hom.: 2148 Cov.: 33 AF XY: 0.0911 AC XY: 6777 AN XY: 74428

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.0421

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00575

Gnomad4 OTH AF: 0.0773

Alfa AF: 0.0544 Hom.: 147

Bravo AF: 0.109

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.5
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485706; hg19: chr20-6849366;