rs6116492

Variant names:

• chr20-4717980-G-T
• rs6116492

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 0.0671 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.195 AC: 8088 AN: 41546

American (AMR) AF: 0.0334 AC: 511 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4822

European-Finnish (FIN) AF: 0.00443 AC: 47 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0192 AC: 1303 AN: 68034

Other (OTH) AF: 0.0535 AC: 113 AN: 2114

Alfa AF: 0.0370 Hom.: 660

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs6116492; hg19: chr20-4698626;