6-11084321-G-C

Variant names:

• chr6-11084321-G-C
• rs4713169

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 0.455 in 152,072 control chromosomes in the GnomAD database, including 16,780 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 0.45 (16780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 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: 0.455 AC: 69120 AN: 151954 Hom.: 16753 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.455 AC: 69184 AN: 152072 Hom.: 16780 Cov.: 32 AF XY: 0.464 AC XY: 34516 AN XY: 74332

African (AFR) AF: 0.359 AC: 14908 AN: 41476

American (AMR) AF: 0.591 AC: 9021 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2002 AN: 3468

East Asian (EAS) AF: 0.904 AC: 4676 AN: 5172

South Asian (SAS) AF: 0.640 AC: 3088 AN: 4826

European-Finnish (FIN) AF: 0.475 AC: 5024 AN: 10574

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29115 AN: 67970

Other (OTH) AF: 0.472 AC: 995 AN: 2108

Alfa AF: 0.437 Hom.: 1851

Bravo AF: 0.459

Asia WGS AF: 0.710 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.53
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs4713169; hg19: chr6-11084554;