6-132564197-A-G

Variant names:

• chr6-132564197-A-G
• rs1361280

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 0.454 in 151,896 control chromosomes in the GnomAD database, including 16,280 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 (16280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 1 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 = 0.83 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68866 AN: 151778 Hom.: 16270 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.454 AC: 68906 AN: 151896 Hom.: 16280 Cov.: 31 AF XY: 0.456 AC XY: 33865 AN XY: 74218

African (AFR) AF: 0.433 AC: 17942 AN: 41434

American (AMR) AF: 0.407 AC: 6220 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1622 AN: 3470

East Asian (EAS) AF: 0.851 AC: 4361 AN: 5126

South Asian (SAS) AF: 0.550 AC: 2648 AN: 4816

European-Finnish (FIN) AF: 0.391 AC: 4118 AN: 10528

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30511 AN: 67946

Other (OTH) AF: 0.470 AC: 991 AN: 2108

Alfa AF: 0.448 Hom.: 2580

Bravo AF: 0.456

Asia WGS AF: 0.700 AC: 2432 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	4.0
DANN	Benign	0.49
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1361280; hg19: chr6-132885336;