rs12535708

Variant names:

• chr7-128238045-C-A
• rs12535708

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 0.305 in 152,132 control chromosomes in the GnomAD database, including 7,643 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 0.31 (7643 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46391 AN: 152014 Hom.: 7639 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.305 AC: 46422 AN: 152132 Hom.: 7643 Cov.: 33 AF XY: 0.303 AC XY: 22554 AN XY: 74346

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.310

Alfa AF: 0.342 Hom.: 1164

Bravo AF: 0.305

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12535708; hg19: chr7-127878098;