rs6042588

Variant names:

• chr20-1492751-A-G
• rs6042588

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 0.195 in 152,160 control chromosomes in the GnomAD database, including 4,875 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 0.19 (4875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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: 0.195 AC: 29595 AN: 152042 Hom.: 4870 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0834

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.195 AC: 29645 AN: 152160 Hom.: 4875 Cov.: 32 AF XY: 0.191 AC XY: 14182 AN XY: 74400

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0834

Gnomad4 NFE AF: 0.0968

Gnomad4 OTH AF: 0.176

Alfa AF: 0.153 Hom.: 516

Bravo AF: 0.207

Asia WGS AF: 0.0840 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6042588; hg19: chr20-1473397;