rs12539316

Variant names:

• chr7-73563568-A-G
• rs12539316

Your query was ambiguous. Multiple possible variants found:

• chr7-73563568-A-G
• chr7-73563568-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;