chr12-34246100-G-C

Variant names:

• chr12-34246100-G-C
• rs10506121

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 0.276 in 152,044 control chromosomes in the GnomAD database, including 7,292 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 0.28 (7292 hom., cov: 32)
• Consequence: AK6P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 3 publications found

Genes affected

AK6P1 (HGNC:51678): (adenylate kinase 6 pseudogene 1)

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 (NFE) allele frequency at 95% confidence interval = 0.378 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: 0.276 AC: 41935 AN: 151926 Hom.: 7290 Cov.: 32

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.276 AC: 41930 AN: 152044 Hom.: 7292 Cov.: 32 AF XY: 0.276 AC XY: 20485 AN XY: 74288

African (AFR) AF: 0.0919 AC: 3814 AN: 41512

American (AMR) AF: 0.263 AC: 4011 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3468

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5180

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4818

European-Finnish (FIN) AF: 0.457 AC: 4828 AN: 10556

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25956 AN: 67930

Other (OTH) AF: 0.265 AC: 560 AN: 2114

Alfa AF: 0.189 Hom.: 434

Bravo AF: 0.257

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.82
DANN	Benign	0.24
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10506121; hg19: chr12-34399035;