6-154633286-C-T

Variant names:

• chr6-154633286-C-T
• rs12523822

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 0.349 in 152,018 control chromosomes in the GnomAD database, including 9,419 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 0.35 (9419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 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: 0.348 AC: 52933 AN: 151898 Hom.: 9403 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.349 AC: 52988 AN: 152018 Hom.: 9419 Cov.: 32 AF XY: 0.349 AC XY: 25904 AN XY: 74296

African (AFR) AF: 0.405 AC: 16780 AN: 41456

American (AMR) AF: 0.311 AC: 4752 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1616 AN: 5162

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3910 AN: 10560

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22375 AN: 67970

Other (OTH) AF: 0.362 AC: 764 AN: 2108

Alfa AF: 0.314 Hom.: 5802

Bravo AF: 0.347

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.66
DANN	Benign	0.60
PhyloP100		-0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12523822;

hg19: chr6-154954420;