NM_001080418.3:c.1107+1447G>T

Variant names:

• chr1-34902830-C-A
• rs11264172
• NM_001080418.3:c.1107+1447G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001080418.3(DLGAP3):​c.1107+1447G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,932 control chromosomes in the GnomAD database, including 12,468 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 0.40 (12468 hom., cov: 31)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP3	NM_001080418.3	c.1107+1447G>T		intron_variant	Intron 3 of 11	ENST00000373347.6	NP_001073887.1
DLGAP3	XM_011541879.3	c.1107+1447G>T		intron_variant	Intron 4 of 12		XP_011540181.1
DLGAP3	XM_047426631.1	c.1107+1447G>T		intron_variant	Intron 3 of 11		XP_047282587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP3	ENST00000373347.6	c.1107+1447G>T		intron_variant	Intron 3 of 11	5	NM_001080418.3	ENSP00000362444.1
DLGAP3	ENST00000235180.4	c.1107+1447G>T		intron_variant	Intron 1 of 9	2		ENSP00000235180.4

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61341 AN: 151814 Hom.: 12453 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.404 AC: 61379 AN: 151932 Hom.: 12468 Cov.: 31 AF XY: 0.403 AC XY: 29894 AN XY: 74230

African (AFR) AF: 0.351 AC: 14563 AN: 41450

American (AMR) AF: 0.381 AC: 5817 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3464

East Asian (EAS) AF: 0.399 AC: 2050 AN: 5144

South Asian (SAS) AF: 0.570 AC: 2749 AN: 4824

European-Finnish (FIN) AF: 0.350 AC: 3696 AN: 10566

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29760 AN: 67900

Other (OTH) AF: 0.423 AC: 890 AN: 2104

Alfa AF: 0.422 Hom.: 17302

Bravo AF: 0.398

Asia WGS AF: 0.489 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	16
DANN	Benign	0.90
PhyloP100		0.63
Mutation Taster		=99/1	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: rs11264172; hg19: chr1-35368431; COSMIC: COSV52392552; COSMIC: COSV52392552;