20-6946028-T-C

Variant names:

• chr20-6946028-T-C
• rs10485708

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 0.265 in 151,998 control chromosomes in the GnomAD database, including 5,978 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 0.27 (5978 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 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: 0.265 AC: 40267 AN: 151880 Hom.: 5967 Cov.: 33

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.265 AC: 40318 AN: 151998 Hom.: 5978 Cov.: 33 AF XY: 0.260 AC XY: 19329 AN XY: 74284

African (AFR) AF: 0.390 AC: 16159 AN: 41462

American (AMR) AF: 0.198 AC: 3032 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3472

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5178

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4818

European-Finnish (FIN) AF: 0.270 AC: 2849 AN: 10542

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15876 AN: 67928

Other (OTH) AF: 0.215 AC: 455 AN: 2112

Alfa AF: 0.231 Hom.: 18140

Bravo AF: 0.263

Asia WGS AF: 0.164 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.51
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10485708; hg19: chr20-6926675;