chr7-128238282-C-A

Variant names:

• chr7-128238282-C-A
• rs12535747

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;