rs6128532

Positions:

• chr20-59292423-G-A
• chr20-59292423-G-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 0.514 in 152,030 control chromosomes in the GnomAD database, including 20,588 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 0.51 (20588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78031 AN: 151912 Hom.: 20577 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.514 AC: 78085 AN: 152030 Hom.: 20588 Cov.: 32 AF XY: 0.522 AC XY: 38824 AN XY: 74314

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.527

Alfa AF: 0.495 Hom.: 10546

Bravo AF: 0.512

Asia WGS AF: 0.777 AC: 2699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6128532; hg19: chr20-57867478;