6-3058456-T-C

Variant names:

• chr6-3058456-T-C
• rs12200314

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 0.421 in 152,120 control chromosomes in the GnomAD database, including 16,272 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 0.42 (16272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 16 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 (NFE) allele frequency at 95% confidence interval = 0.565 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: 0.422 AC: 64096 AN: 152002 Hom.: 16267 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.421 AC: 64112 AN: 152120 Hom.: 16272 Cov.: 32 AF XY: 0.421 AC XY: 31326 AN XY: 74356

African (AFR) AF: 0.134 AC: 5580 AN: 41508

American (AMR) AF: 0.452 AC: 6904 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1608 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1999 AN: 5176

South Asian (SAS) AF: 0.372 AC: 1799 AN: 4830

European-Finnish (FIN) AF: 0.596 AC: 6305 AN: 10572

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.569 AC: 38696 AN: 67968

Other (OTH) AF: 0.422 AC: 894 AN: 2116

Alfa AF: 0.506 Hom.: 40211

Bravo AF: 0.398

Asia WGS AF: 0.354 AC: 1232 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	1.5
DANN	Benign	0.85
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs12200314; hg19: chr6-3058690;