chr6-135132889-C-A

Variant names:

• chr6-135132889-C-A
• rs6929404

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 0.282 in 152,006 control chromosomes in the GnomAD database, including 6,416 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 0.28 (6416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.281 AC: 42753 AN: 151888 Hom.: 6392 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.282 AC: 42839 AN: 152006 Hom.: 6416 Cov.: 32 AF XY: 0.287 AC XY: 21311 AN XY: 74290

African (AFR) AF: 0.367 AC: 15193 AN: 41418

American (AMR) AF: 0.274 AC: 4184 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1810 AN: 5174

South Asian (SAS) AF: 0.418 AC: 2021 AN: 4832

European-Finnish (FIN) AF: 0.278 AC: 2938 AN: 10552

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15100 AN: 67974

Other (OTH) AF: 0.300 AC: 633 AN: 2112

Alfa AF: 0.244 Hom.: 930

Bravo AF: 0.285

Asia WGS AF: 0.433 AC: 1505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.17
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6929404; hg19: chr6-135454027;