rs12579938

Positions:

• chr12-31644861-G-A
• chr12-31644861-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000418260.3(AK4P3):​c.-184+6875C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,088 control chromosomes in the GnomAD database, including 30,356 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 0.63 (30356 hom., cov: 33)
• Consequence: AK4P3 ENST00000418260.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

Genes affected

AK4P3 (HGNC:21596): (adenylate kinase 4 pseudogene 3)

LOC124902913 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902913	XR_007063269.1	n.323+6875C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AK4P3	ENST00000418260.3	c.-184+6875C>T		intron_variant				ENSP00000510584	P1
AK4P3	ENST00000659799.1	n.360+6875C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95696 AN: 151970 Hom.: 30311 Cov.: 33

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.630 AC: 95801 AN: 152088 Hom.: 30356 Cov.: 33 AF XY: 0.627 AC XY: 46596 AN XY: 74340

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.643

Alfa AF: 0.637 Hom.: 40598

Bravo AF: 0.640

Asia WGS AF: 0.499 AC: 1736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12579938; hg19: chr12-31797795;