rs12706933

Positions:

• chr7-130468307-G-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 0.319 in 151,620 control chromosomes in the GnomAD database, including 9,557 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 0.32 (9557 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.319 AC: 48277 AN: 151500 Hom.: 9544 Cov.: 31

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.319 AC: 48301 AN: 151620 Hom.: 9557 Cov.: 31 AF XY: 0.326 AC XY: 24176 AN XY: 74104

Gnomad4 AFR AF: 0.0865

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.369

Alfa AF: 0.370 Hom.: 5150

Bravo AF: 0.319

Asia WGS AF: 0.605 AC: 2098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
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: rs12706933; hg19: chr7-130108148;