chr6-135132889-C-A

Position:

• chr6-135132889-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.300

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6929404; hg19: chr6-135454027;