6-33150041-C-T

Position:

• chr6-33150041-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 0.194 in 152,084 control chromosomes in the GnomAD database, including 3,378 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 0.19 (3378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.194 AC: 29445 AN: 151966 Hom.: 3365 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.194 AC: 29480 AN: 152084 Hom.: 3378 Cov.: 32 AF XY: 0.198 AC XY: 14688 AN XY: 74330

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.208

Alfa AF: 0.183 Hom.: 3924

Bravo AF: 0.205

Asia WGS AF: 0.253 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0080
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs721394; hg19: chr6-33117818;