rs7299940

Positions:

• chr12-130906209-C-G

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 0.588 in 152,058 control chromosomes in the GnomAD database, including 27,147 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 0.59 (27147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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: 0.588 AC: 89367 AN: 151940 Hom.: 27136 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.588 AC: 89421 AN: 152058 Hom.: 27147 Cov.: 32 AF XY: 0.584 AC XY: 43407 AN XY: 74328

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.585

Alfa AF: 0.580 Hom.: 3235

Bravo AF: 0.598

Asia WGS AF: 0.323 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.26
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7299940; hg19: chr12-131390754;