rs11051507

Variant names:

• chr12-31642430-C-A
• rs11051507
• ENST00000418260.3:c.-184+9306G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-31642430-C-A
• chr12-31642430-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

DENND5B-AS1 (HGNC:42517): (DENND5B antisense RNA 1)

LOC124902913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124902913	XR_007063269.1	n.323+9306G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AK4P3	ENST00000418260.3	c.-184+9306G>T		intron_variant	Intron 1 of 1	6		ENSP00000510584.1
DENND5B-AS1	ENST00000784765.1	n.1934C>A		non_coding_transcript_exon_variant	Exon 5 of 5
AK4P3	ENST00000659799.1	n.360+9306G>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.415 AC: 17153 AN: 41370

American (AMR) AF: 0.686 AC: 10469 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3466

East Asian (EAS) AF: 0.760 AC: 3933 AN: 5172

South Asian (SAS) AF: 0.775 AC: 3740 AN: 4828

European-Finnish (FIN) AF: 0.816 AC: 8636 AN: 10578

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50002 AN: 67960

Other (OTH) AF: 0.666 AC: 1405 AN: 2110

Alfa AF: 0.709 Hom.: 17832

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
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs11051507; hg19: chr12-31795364;