rs6124036

Variant names:

• chr20-60942423-A-G
• rs6124036

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 0.0855 in 152,228 control chromosomes in the GnomAD database, including 1,757 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 0.085 (1757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11

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 (EAS) allele frequency at 95% confidence interval = 0.582 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: 0.0853 AC: 12982 AN: 152110 Hom.: 1747 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0855 AC: 13015 AN: 152228 Hom.: 1757 Cov.: 32 AF XY: 0.0917 AC XY: 6829 AN XY: 74438

Gnomad4 AFR AF: 0.0965

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.0569

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0145

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0812 Hom.: 260

Bravo AF: 0.110

Asia WGS AF: 0.265 AC: 920 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	1.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6124036; hg19: chr20-59517479;