rs870384

Variant names:

• chr12-73076266-G-A
• rs870384

Your query was ambiguous. Multiple possible variants found:

• chr12-73076266-G-A
• chr12-73076266-G-C

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 0.396 in 151,980 control chromosomes in the GnomAD database, including 14,728 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 0.40 (14728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 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: 0.396 AC: 60063 AN: 151862 Hom.: 14695 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.396 AC: 60148 AN: 151980 Hom.: 14728 Cov.: 32 AF XY: 0.394 AC XY: 29289 AN XY: 74288

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.364

Alfa AF: 0.159 Hom.: 270

Bravo AF: 0.411

Asia WGS AF: 0.268 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.55
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs870384; hg19: chr12-73470046;