rs7299940

Variant names:

• chr12-130906209-C-G
• rs7299940

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.718 AC: 29782 AN: 41472

American (AMR) AF: 0.584 AC: 8924 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2000 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1445 AN: 5172

South Asian (SAS) AF: 0.358 AC: 1727 AN: 4820

European-Finnish (FIN) AF: 0.582 AC: 6146 AN: 10562

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37454 AN: 67980

Other (OTH) AF: 0.585 AC: 1232 AN: 2106

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7299940; hg19: chr12-131390754;