14-55182172-A-T

Variant names:

• chr14-55182172-A-T
• rs7155936
• NM_014750.5:c.495+198T>A

Variant summary

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

The NM_014750.5(DLGAP5):​c.495+198T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0825 in 152,248 control chromosomes in the GnomAD database, including 1,394 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 0.083 (1394 hom., cov: 32)
• Consequence: DLGAP5 NM_014750.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP5	NM_014750.5	c.495+198T>A		intron_variant	Intron 4 of 18	ENST00000247191.7	NP_055565.3
DLGAP5	NM_001146015.2	c.495+198T>A		intron_variant	Intron 4 of 19		NP_001139487.1
DLGAP5	XM_017021840.3	c.495+198T>A		intron_variant	Intron 4 of 18		XP_016877329.1
DLGAP5	XM_047432016.1	c.495+198T>A		intron_variant	Intron 4 of 19		XP_047287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP5	ENST00000247191.7	c.495+198T>A		intron_variant	Intron 4 of 18	1	NM_014750.5	ENSP00000247191.2
DLGAP5	ENST00000395425.6	c.495+198T>A		intron_variant	Intron 4 of 19	1		ENSP00000378815.2
DLGAP5	ENST00000557645.5	c.495+198T>A		intron_variant	Intron 4 of 5	3		ENSP00000451747.1

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12527 AN: 152130 Hom.: 1385 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.00518

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.00784

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0825 AC: 12565 AN: 152248 Hom.: 1394 Cov.: 32 AF XY: 0.0803 AC XY: 5981 AN XY: 74442

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.0445

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.0643

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.00518

Gnomad4 NFE AF: 0.00784

Gnomad4 OTH AF: 0.0747

Alfa AF: 0.0134 Hom.: 29

Bravo AF: 0.0917

Asia WGS AF: 0.0840 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.52

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: rs7155936; hg19: chr14-55648890;