11-77264422-T-C

Position:

• chr11-77264422-T-C

Variant summary

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

The NM_182833.3(GDPD4):​c.707+4035A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,810 control chromosomes in the GnomAD database, including 25,019 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 0.57 (25019 hom., cov: 31)
• Consequence: GDPD4 NM_182833.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

Genes affected

GDPD4 (HGNC:24849): (glycerophosphodiester phosphodiesterase domain containing 4) Predicted to enable metal ion binding activity and phosphoric diester hydrolase activity. Predicted to be involved in lipid metabolic process. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GDPD4	NM_182833.3	c.707+4035A>G		intron_variant		ENST00000315938.5	NP_878253.1
GDPD4	XM_011544834.1	c.785+4035A>G		intron_variant			XP_011543136.1
GDPD4	XM_047426557.1	c.416+4035A>G		intron_variant			XP_047282513.1
GDPD4	XM_047426558.1	c.416+4035A>G		intron_variant			XP_047282514.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GDPD4	ENST00000315938.5	c.707+4035A>G		intron_variant		1	NM_182833.3	ENSP00000320815.4
GDPD4	ENST00000376217.6	c.707+4035A>G		intron_variant		1		ENSP00000365390.2

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86247 AN: 151692 Hom.: 24999 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.569 AC: 86311 AN: 151810 Hom.: 25019 Cov.: 31 AF XY: 0.571 AC XY: 42392 AN XY: 74196

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.582

Alfa AF: 0.590 Hom.: 3236

Bravo AF: 0.562

Asia WGS AF: 0.471 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.78

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: rs1793483; hg19: chr11-76975467;