6-133901115-C-T

Variant names:

• chr6-133901115-C-T
• rs328455

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 0.939 in 152,262 control chromosomes in the GnomAD database, including 67,210 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 0.94 (67210 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

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 (AFR) allele frequency at 95% confidence interval = 0.976 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: 0.939 AC: 142864 AN: 152144 Hom.: 67149 Cov.: 32

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.939 AC: 142984 AN: 152262 Hom.: 67210 Cov.: 32 AF XY: 0.938 AC XY: 69834 AN XY: 74416

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.960

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.941

Alfa AF: 0.926 Hom.: 8117

Bravo AF: 0.947

Asia WGS AF: 0.934 AC: 3249 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	2.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs328455; hg19: chr6-134222253;