rs12535708

Positions:

• chr7-128238045-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 0.305 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;