6-33017422-C-T

Variant names:

• chr6-33017422-C-T
• rs1367731

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0738 AC: 3062 AN: 41508

American (AMR) AF: 0.134 AC: 2052 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3470

East Asian (EAS) AF: 0.178 AC: 920 AN: 5172

South Asian (SAS) AF: 0.207 AC: 997 AN: 4820

European-Finnish (FIN) AF: 0.170 AC: 1792 AN: 10560

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10926 AN: 67978

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.147 Hom.: 6442

Bravo AF: 0.129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1367731; hg19: chr6-32985199;