chr12-73076266-G-A

Variant names:

• chr12-73076266-G-A
• rs870384

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 0.396 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.696 AC: 28852 AN: 41440

American (AMR) AF: 0.335 AC: 5110 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3470

East Asian (EAS) AF: 0.0992 AC: 513 AN: 5170

South Asian (SAS) AF: 0.363 AC: 1741 AN: 4794

European-Finnish (FIN) AF: 0.282 AC: 2976 AN: 10570

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19027 AN: 67954

Other (OTH) AF: 0.364 AC: 769 AN: 2110

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs870384; hg19: chr12-73470046;