rs6116492

chr20-4717980-G-T

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 0.0671 in 152,288 control chromosomes in the GnomAD database, including 826 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 0.067 (826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 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: 0.0669 AC: 10178 AN: 152170 Hom.: 820 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0671 AC: 10217 AN: 152288 Hom.: 826 Cov.: 32 AF XY: 0.0640 AC XY: 4767 AN XY: 74468

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.00443

Gnomad4 NFE AF: 0.0192

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0266 Hom.: 115

Bravo AF: 0.0732

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.0
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6116492; hg19: chr20-4698626;