6-132578260-G-A

Variant names:

• chr6-132578260-G-A
• rs6937506

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 0.251 in 152,016 control chromosomes in the GnomAD database, including 5,447 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 0.25 (5447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38040 AN: 151896 Hom.: 5434 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.251 AC: 38098 AN: 152016 Hom.: 5447 Cov.: 32 AF XY: 0.248 AC XY: 18446 AN XY: 74302

African (AFR) AF: 0.381 AC: 15760 AN: 41414

American (AMR) AF: 0.241 AC: 3681 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3466

East Asian (EAS) AF: 0.150 AC: 775 AN: 5182

South Asian (SAS) AF: 0.147 AC: 710 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2466 AN: 10560

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13318 AN: 67980

Other (OTH) AF: 0.231 AC: 487 AN: 2112

Alfa AF: 0.227 Hom.: 1589

Bravo AF: 0.258

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.63
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6937506; hg19: chr6-132899399;