9-83753559-G-C

Variant names:

• chr9-83753559-G-C
• rs7044691
• NM_025211.4:c.739-200C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025211.4(GKAP1):​c.739-200C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,992 control chromosomes in the GnomAD database, including 24,763 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 0.56 (24763 hom., cov: 32)
• Consequence: GKAP1 NM_025211.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 3 publications found

Genes affected

GKAP1 (HGNC:17496): (G kinase anchoring protein 1) This gene encodes a protein that is highly similar to the mouse cGMP-dependent protein kinase anchoring protein 42kDa. The mouse protein has been found to localize with the Golgi and recruit cGMP-dependent protein kinase I alpha to the Golgi in mouse testes. It is thought to play a role in germ cell development. Transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GKAP1	NM_025211.4	c.739-200C>G		intron_variant	Intron 8 of 12	ENST00000376371.7	NP_079487.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GKAP1	ENST00000376371.7	c.739-200C>G		intron_variant	Intron 8 of 12	1	NM_025211.4	ENSP00000365550.2
GKAP1	ENST00000376365.7	c.586-200C>G		intron_variant	Intron 7 of 11	1		ENSP00000365544.3

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85645 AN: 151874 Hom.: 24743 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.564 AC: 85698 AN: 151992 Hom.: 24763 Cov.: 32 AF XY: 0.563 AC XY: 41811 AN XY: 74298

African (AFR) AF: 0.445 AC: 18459 AN: 41464

American (AMR) AF: 0.696 AC: 10639 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2154 AN: 3466

East Asian (EAS) AF: 0.622 AC: 3207 AN: 5160

South Asian (SAS) AF: 0.531 AC: 2562 AN: 4824

European-Finnish (FIN) AF: 0.585 AC: 6154 AN: 10524

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.596 AC: 40483 AN: 67958

Other (OTH) AF: 0.580 AC: 1223 AN: 2108

Alfa AF: 0.553 Hom.: 2822

Bravo AF: 0.571

Asia WGS AF: 0.590 AC: 2041 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		-0.096
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7044691; hg19: chr9-86368474;