12-94135049-A-G

Variant names:

• chr12-94135049-A-G
• rs3847794

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 0.259 in 152,174 control chromosomes in the GnomAD database, including 6,454 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 0.26 (6454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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: 0.259 AC: 39409 AN: 152054 Hom.: 6452 Cov.: 32

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.259 AC: 39414 AN: 152174 Hom.: 6454 Cov.: 32 AF XY: 0.256 AC XY: 19034 AN XY: 74368

African (AFR) AF: 0.0673 AC: 2797 AN: 41548

American (AMR) AF: 0.348 AC: 5329 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3470

East Asian (EAS) AF: 0.111 AC: 577 AN: 5190

South Asian (SAS) AF: 0.137 AC: 662 AN: 4824

European-Finnish (FIN) AF: 0.354 AC: 3738 AN: 10566

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24255 AN: 67968

Other (OTH) AF: 0.246 AC: 521 AN: 2114

Alfa AF: 0.316 Hom.: 8850

Bravo AF: 0.251

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.73
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs3847794; hg19: chr12-94528825;