rs12535747

chr7-128238282-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 0.299 in 151,962 control chromosomes in the GnomAD database, including 7,487 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 0.30 (7487 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45427 AN: 151844 Hom.: 7486 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.299 AC: 45443 AN: 151962 Hom.: 7487 Cov.: 32 AF XY: 0.297 AC XY: 22085 AN XY: 74270

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.308

Alfa AF: 0.316 Hom.: 1177

Bravo AF: 0.298

Asia WGS AF: 0.224 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12535747; hg19: chr7-127878335;