chr6-33017422-C-T

Variant names:

• chr6-33017422-C-T
• rs1367731

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 0.137 in 152,106 control chromosomes in the GnomAD database, including 1,619 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 0.14 (1619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 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: 0.137 AC: 20779 AN: 151988 Hom.: 1613 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.137 AC: 20786 AN: 152106 Hom.: 1619 Cov.: 32 AF XY: 0.138 AC XY: 10257 AN XY: 74330

Gnomad4 AFR AF: 0.0738

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.132

Alfa AF: 0.149 Hom.: 2606

Bravo AF: 0.129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1367731; hg19: chr6-32985199;