rs11051507

chr12-31642430-C-Achr12-31642430-C-G

Variant summary

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

The ENST00000418260.3(AK4P3):c.-184+9306G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,952 control chromosomes in the GnomAD database, including 33,995 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 0.65 (33995 hom., cov: 33)
• Consequence: AK4P3 ENST00000418260.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643

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=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902913	XR_007063269.1	n.323+9306G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AK4P3	ENST00000418260.3	c.-184+9306G>T		intron_variant				P1
AK4P3	ENST00000659799.1	n.360+9306G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98947 AN: 151834 Hom.: 33984 Cov.: 33

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.651 AC: 98991 AN: 151952 Hom.: 33995 Cov.: 33 AF XY: 0.658 AC XY: 48866 AN XY: 74280

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.666

Alfa AF: 0.710 Hom.: 15700

Bravo AF: 0.627

Asia WGS AF: 0.753 AC: 2620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	5.1
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11051507; hg19: chr12-31795364;