1-34908277-G-T

Position:

• chr1-34908277-G-T

Variant summary

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

The NM_001080418.3(DLGAP3):​c.-134-840C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,086 control chromosomes in the GnomAD database, including 20,976 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 0.52 (20976 hom., cov: 33)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

Genes affected

DLGAP3 (HGNC:30368): (DLG associated protein 3) Predicted to enable PDZ domain binding activity; molecular adaptor activity; and scaffold protein binding activity. Predicted to be involved in protein-containing complex assembly and regulation of postsynaptic neurotransmitter receptor activity. Predicted to be located in synapse. Predicted to be part of postsynaptic density. Predicted to be active in several cellular components, including cholinergic synapse; glutamatergic synapse; and neuromuscular junction. [provided by Alliance of Genome Resources, Apr 2022]

DLGAP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLGAP3	NM_001080418.3	c.-134-840C>A		intron_variant		ENST00000373347.6	NP_001073887.1
DLGAP3	XM_011541879.3	c.-134-840C>A		intron_variant			XP_011540181.1
DLGAP3	XM_047426631.1	c.-134-840C>A		intron_variant			XP_047282587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLGAP3	ENST00000373347.6	c.-134-840C>A		intron_variant		5	NM_001080418.3	ENSP00000362444.1
DLGAP3	ENST00000495979.1	n.122-840C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78623 AN: 151968 Hom.: 20965 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.517 AC: 78668 AN: 152086 Hom.: 20976 Cov.: 33 AF XY: 0.515 AC XY: 38265 AN XY: 74342

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.518

Alfa AF: 0.566 Hom.: 31912

Bravo AF: 0.501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.54

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: rs7555884; hg19: chr1-35373878;