6-20533152-G-T

Position:

• chr6-20533152-G-T

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 0.243 in 151,662 control chromosomes in the GnomAD database, including 5,465 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 0.24 (5465 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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: 0.243 AC: 36816 AN: 151544 Hom.: 5463 Cov.: 29

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.243 AC: 36817 AN: 151662 Hom.: 5465 Cov.: 29 AF XY: 0.251 AC XY: 18580 AN XY: 74080

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.260

Alfa AF: 0.276 Hom.: 6446

Bravo AF: 0.237

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
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: rs9368197; hg19: chr6-20533383;