rs6036007

Variant names:

• chr20-21993952-T-C
• rs6036007

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 0.531 in 151,906 control chromosomes in the GnomAD database, including 22,400 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 0.53 (22400 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 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: 0.530 AC: 80515 AN: 151788 Hom.: 22344 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.531 AC: 80629 AN: 151906 Hom.: 22400 Cov.: 31 AF XY: 0.528 AC XY: 39191 AN XY: 74236

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.545

Alfa AF: 0.489 Hom.: 2360

Bravo AF: 0.558

Asia WGS AF: 0.579 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6036007; hg19: chr20-21974590;