1-34903170-A-G

Position:

• chr1-34903170-A-G

Variant summary

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

The NM_001080418.3(DLGAP3):​c.1107+1107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,062 control chromosomes in the GnomAD database, including 9,520 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 0.35 (9520 hom., cov: 32)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLGAP3	NM_001080418.3	c.1107+1107T>C		intron_variant		ENST00000373347.6
DLGAP3	XM_011541879.3	c.1107+1107T>C		intron_variant
DLGAP3	XM_047426631.1	c.1107+1107T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLGAP3	ENST00000373347.6	c.1107+1107T>C		intron_variant		5	NM_001080418.3	P1
DLGAP3	ENST00000235180.4	c.1107+1107T>C		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52525 AN: 151944 Hom.: 9519 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.346 AC: 52547 AN: 152062 Hom.: 9520 Cov.: 32 AF XY: 0.344 AC XY: 25550 AN XY: 74346

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.0406

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.370

Alfa AF: 0.364 Hom.: 10454

Bravo AF: 0.342

Asia WGS AF: 0.164 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs11264173; hg19: chr1-35368771;