rs16837122

Variant names:

• chr1-34912977-C-G
• rs16837122
• NM_001080418.3:c.-134-5540G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-34912977-C-G
• chr1-34912977-C-T

Variant summary

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

The NM_001080418.3(DLGAP3):​c.-134-5540G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,194 control chromosomes in the GnomAD database, including 2,808 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 0.19 (2808 hom., cov: 32)
• Consequence: DLGAP3 NM_001080418.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP3	NM_001080418.3	c.-134-5540G>C		intron_variant	Intron 1 of 11	ENST00000373347.6	NP_001073887.1
DLGAP3	XM_011541879.3	c.-134-5540G>C		intron_variant	Intron 2 of 12		XP_011540181.1
DLGAP3	XM_047426631.1	c.-134-5540G>C		intron_variant	Intron 1 of 11		XP_047282587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP3	ENST00000373347.6	c.-134-5540G>C		intron_variant	Intron 1 of 11	5	NM_001080418.3	ENSP00000362444.1
DLGAP3	ENST00000495979.1	n.122-5540G>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28504 AN: 152076 Hom.: 2803 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.187 AC: 28528 AN: 152194 Hom.: 2808 Cov.: 32 AF XY: 0.186 AC XY: 13821 AN XY: 74414

African (AFR) AF: 0.187 AC: 7764 AN: 41518

American (AMR) AF: 0.229 AC: 3493 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3470

East Asian (EAS) AF: 0.0150 AC: 78 AN: 5184

South Asian (SAS) AF: 0.118 AC: 568 AN: 4826

European-Finnish (FIN) AF: 0.157 AC: 1664 AN: 10606

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13408 AN: 67996

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.0904 Hom.: 114

Bravo AF: 0.195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		0.13
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: rs16837122; hg19: chr1-35378578;