6-34227089-C-T

Variant names:

• chr6-34227089-C-T
• rs1759645

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 0.713 in 152,024 control chromosomes in the GnomAD database, including 41,089 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 0.71 (41089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108348 AN: 151906 Hom.: 41089 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.713 AC: 108381 AN: 152024 Hom.: 41089 Cov.: 32 AF XY: 0.718 AC XY: 53396 AN XY: 74328

African (AFR) AF: 0.436 AC: 18046 AN: 41394

American (AMR) AF: 0.669 AC: 10216 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2791 AN: 3466

East Asian (EAS) AF: 0.875 AC: 4514 AN: 5160

South Asian (SAS) AF: 0.892 AC: 4305 AN: 4824

European-Finnish (FIN) AF: 0.870 AC: 9228 AN: 10602

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56799 AN: 67990

Other (OTH) AF: 0.716 AC: 1513 AN: 2114

Alfa AF: 0.781 Hom.: 128710

Bravo AF: 0.679

Asia WGS AF: 0.809 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.48
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs1759645; hg19: chr6-34194866;