20-46006464-C-T

Variant names:

• chr20-46006464-C-T
• rs6065913

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 0.355 in 152,002 control chromosomes in the GnomAD database, including 10,171 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 0.35 (10171 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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: 0.355 AC: 53870 AN: 151884 Hom.: 10169 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.355 AC: 53898 AN: 152002 Hom.: 10171 Cov.: 32 AF XY: 0.361 AC XY: 26799 AN XY: 74298

African (AFR) AF: 0.308 AC: 12773 AN: 41436

American (AMR) AF: 0.270 AC: 4128 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3746 AN: 5172

South Asian (SAS) AF: 0.455 AC: 2192 AN: 4822

European-Finnish (FIN) AF: 0.416 AC: 4386 AN: 10542

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24200 AN: 67966

Other (OTH) AF: 0.344 AC: 725 AN: 2108

Alfa AF: 0.349 Hom.: 3495

Bravo AF: 0.342

Asia WGS AF: 0.527 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.8
DANN	Benign	0.53
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs6065913; hg19: chr20-44635103;