rs119672

Variant names:

• chr17-19915288-A-C
• rs119672
• NM_007202.4:c.1834+4748T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-19915288-A-C
• chr17-19915288-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_007202.4(AKAP10):​c.1834+4748T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: AKAP10 NM_007202.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

AKAP10 (HGNC:368): (A-kinase anchoring protein 10) This gene encodes a member of the A-kinase anchor protein family. A-kinase anchor proteins bind to the regulatory subunits of protein kinase A (PKA) and confine the holoenzyme to discrete locations within the cell. The encoded protein is localized to mitochondria and interacts with both the type I and type II regulatory subunits of PKA. Polymorphisms in this gene may be associated with increased risk of arrhythmias and sudden cardiac death. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP10	NM_007202.4	c.1834+4748T>G		intron_variant	Intron 12 of 14	ENST00000225737.11	NP_009133.2
AKAP10	NM_001330152.2	c.1660+4748T>G		intron_variant	Intron 11 of 13		NP_001317081.1
AKAP10	XR_007065258.1	n.1873+4748T>G		intron_variant	Intron 11 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKAP10	ENST00000225737.11	c.1834+4748T>G		intron_variant	Intron 12 of 14	1	NM_007202.4	ENSP00000225737.6
AKAP10	ENST00000395536.7	c.1660+4748T>G		intron_variant	Intron 11 of 13	5		ENSP00000378907.3
AKAP10	ENST00000583951.1	c.145+4748T>G		intron_variant	Intron 2 of 3	3		ENSP00000463398.1
AKAP10	ENST00000578898.1	n.*167+4748T>G		intron_variant	Intron 3 of 5	3		ENSP00000466329.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs119672; hg19: chr17-19818601;