rs6116477

Variant names:

• chr20-4704015-T-C
• rs6116477

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 0.222 in 152,106 control chromosomes in the GnomAD database, including 4,091 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 0.22 (4091 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.222 AC: 33726 AN: 151988 Hom.: 4081 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.222 AC: 33770 AN: 152106 Hom.: 4091 Cov.: 32 AF XY: 0.215 AC XY: 15957 AN XY: 74348

African (AFR) AF: 0.319 AC: 13223 AN: 41490

American (AMR) AF: 0.207 AC: 3171 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3468

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5174

South Asian (SAS) AF: 0.170 AC: 820 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1242 AN: 10588

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13668 AN: 67968

Other (OTH) AF: 0.222 AC: 467 AN: 2108

Alfa AF: 0.205 Hom.: 2321

Bravo AF: 0.231

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.37
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6116477; hg19: chr20-4684661;