rs12539316

chr7-73563568-A-Gchr7-73563568-A-T

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 0.272 in 151,788 control chromosomes in the GnomAD database, including 5,964 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 0.27 (5964 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.272 AC: 41228 AN: 151676 Hom.: 5939 Cov.: 30

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.272 AC: 41302 AN: 151788 Hom.: 5964 Cov.: 30 AF XY: 0.267 AC XY: 19790 AN XY: 74170

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.246

Alfa AF: 0.268 Hom.: 9187

Bravo AF: 0.274

Asia WGS AF: 0.160 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	0.45
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12539316; hg19: chr7-72977898;