20-46148656-C-T

Variant names:

• chr20-46148656-C-T
• rs6032678

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 0.481 in 151,912 control chromosomes in the GnomAD database, including 18,114 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 0.48 (18114 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72996 AN: 151794 Hom.: 18087 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.481 AC: 73062 AN: 151912 Hom.: 18114 Cov.: 31 AF XY: 0.475 AC XY: 35261 AN XY: 74236

African (AFR) AF: 0.602 AC: 24932 AN: 41418

American (AMR) AF: 0.329 AC: 5033 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1652 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1631 AN: 5154

South Asian (SAS) AF: 0.440 AC: 2121 AN: 4822

European-Finnish (FIN) AF: 0.471 AC: 4974 AN: 10554

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.460 AC: 31201 AN: 67902

Other (OTH) AF: 0.431 AC: 910 AN: 2112

Alfa AF: 0.459 Hom.: 69788

Bravo AF: 0.475

Asia WGS AF: 0.365 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.66
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs6032678; hg19: chr20-44777295;