rs1947234

Variant names:

• chr12-39056689-C-A
• rs1947234

Your query was ambiguous. Multiple possible variants found:

• chr12-39056689-C-A
• chr12-39056689-C-G
• chr12-39056689-C-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 0.288 in 152,082 control chromosomes in the GnomAD database, including 6,626 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 0.29 (6626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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: 0.288 AC: 43691 AN: 151964 Hom.: 6615 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.288 AC: 43740 AN: 152082 Hom.: 6626 Cov.: 32 AF XY: 0.280 AC XY: 20819 AN XY: 74356

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.0856

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.281

Alfa AF: 0.295 Hom.: 14093

Bravo AF: 0.292

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1947234; hg19: chr12-39450491;