6-33497705-C-T

Position:

• chr6-33497705-C-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 0.514 in 152,096 control chromosomes in the GnomAD database, including 22,959 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 (22959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78152 AN: 151978 Hom.: 22955 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.514 AC: 78172 AN: 152096 Hom.: 22959 Cov.: 32 AF XY: 0.528 AC XY: 39220 AN XY: 74320

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.518

Alfa AF: 0.574 Hom.: 11069

Bravo AF: 0.483

Asia WGS AF: 0.782 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9394152; hg19: chr6-33465482;