12-84370421-G-A

Variant names:

• chr12-84370421-G-A
• rs7975057

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 0.458 in 151,800 control chromosomes in the GnomAD database, including 16,643 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 0.46 (16643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69502 AN: 151682 Hom.: 16613 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.458 AC: 69593 AN: 151800 Hom.: 16643 Cov.: 32 AF XY: 0.455 AC XY: 33725 AN XY: 74188

African (AFR) AF: 0.569 AC: 23555 AN: 41418

American (AMR) AF: 0.500 AC: 7619 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1016 AN: 5158

South Asian (SAS) AF: 0.551 AC: 2655 AN: 4820

European-Finnish (FIN) AF: 0.309 AC: 3256 AN: 10542

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28016 AN: 67848

Other (OTH) AF: 0.484 AC: 1021 AN: 2110

Alfa AF: 0.421 Hom.: 1762

Bravo AF: 0.477

Asia WGS AF: 0.401 AC: 1396 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.93
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7975057; hg19: chr12-84764200;