6-33109999-C-T

Variant names:

• chr6-33109999-C-T
• rs6457713

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 0.149 in 140,830 control chromosomes in the GnomAD database, including 2,656 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 0.15 (2656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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: 0.149 AC: 20960 AN: 140740 Hom.: 2651 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.0169

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.149 AC: 20983 AN: 140830 Hom.: 2656 Cov.: 31 AF XY: 0.144 AC XY: 9907 AN XY: 68722

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.0789

Gnomad4 ASJ AF: 0.0377

Gnomad4 EAS AF: 0.0348

Gnomad4 SAS AF: 0.0738

Gnomad4 FIN AF: 0.0579

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0898 Hom.: 1157

Bravo AF: 0.147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6457713; hg19: chr6-33077776;