6-34221089-C-T

Variant names:

• chr6-34221089-C-T
• rs12214804

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 0.808 in 151,810 control chromosomes in the GnomAD database, including 51,185 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 0.81 (51185 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.919 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: 0.809 AC: 122685 AN: 151692 Hom.: 51183 Cov.: 28

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.808 AC: 122724 AN: 151810 Hom.: 51185 Cov.: 28 AF XY: 0.812 AC XY: 60241 AN XY: 74196

African (AFR) AF: 0.601 AC: 24846 AN: 41318

American (AMR) AF: 0.730 AC: 11110 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2918 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4546 AN: 5164

South Asian (SAS) AF: 0.942 AC: 4526 AN: 4804

European-Finnish (FIN) AF: 0.953 AC: 10079 AN: 10578

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 61989 AN: 67938

Other (OTH) AF: 0.798 AC: 1681 AN: 2106

Alfa AF: 0.878 Hom.: 84407

Bravo AF: 0.776

Asia WGS AF: 0.861 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.41
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs12214804; hg19: chr6-34188866;