rs2274273

Variant names:

• chr14-55147918-G-A
• rs2274273
• NM_014750.5:c.*433C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-55147918-G-A
• chr14-55147918-G-C
• chr14-55147918-G-T

Variant summary

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

The NM_014750.5(DLGAP5):​c.*433C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,056 control chromosomes in the GnomAD database, including 12,310 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 (12310 hom., cov: 33)
• Consequence: DLGAP5 NM_014750.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

DLGAP5 (HGNC:16864): (DLG associated protein 5) Predicted to enable microtubule binding activity. Predicted to be involved in several processes, including centrosome localization; kinetochore assembly; and mitotic spindle organization. Located in several cellular components, including centrosome; cytosol; and mitochondrion. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP5	NM_014750.5	c.*433C>T		downstream_gene_variant		ENST00000247191.7	NP_055565.3
DLGAP5	NM_001146015.2	c.*536C>T		downstream_gene_variant			NP_001139487.1
DLGAP5	XM_017021840.3	c.*433C>T		downstream_gene_variant			XP_016877329.1
DLGAP5	XM_047432016.1	c.*536C>T		downstream_gene_variant			XP_047287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP5	ENST00000247191.7	c.*433C>T		downstream_gene_variant		1	NM_014750.5	ENSP00000247191.2
DLGAP5	ENST00000395425.6	c.*536C>T		downstream_gene_variant		1		ENSP00000378815.2

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60242 AN: 151936 Hom.: 12297 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.397 AC: 60294 AN: 152056 Hom.: 12310 Cov.: 33 AF XY: 0.398 AC XY: 29595 AN XY: 74342

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.347

Alfa AF: 0.380 Hom.: 13274

Bravo AF: 0.377

Asia WGS AF: 0.297 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2274273; hg19: chr14-55614636;