rs6116477

Positions:

• chr20-4704015-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 0.222 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.222 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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.222

Alfa AF: 0.203 Hom.: 2018

Bravo AF: 0.231

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6116477; hg19: chr20-4684661;