12-63626530-TA-TAAAA

Position:

• chr12-63626530-TA-TAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_173812.5(DPY19L2):​c.804-7_804-5dupTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.024 (80 hom., cov: 0)
  • Exomes 𝑓: 0.026 (242 hom.)
  • Failed GnomAD Quality Control
• Consequence: DPY19L2 NM_173812.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

Genes affected

DPY19L2 (HGNC:19414): (dpy-19 like 2) The protein encoded by this gene belongs to the dpy-19 family. It is highly expressed in testis, and is required for sperm head elongation and acrosome formation during spermatogenesis. Mutations in this gene are associated with an infertility disorder, spermatogenic failure type 9 (SPGF9). [provided by RefSeq, Dec 2011]

ENSG00000249753 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPY19L2	NM_173812.5	c.804-7_804-5dupTTT		splice_region_variant, intron_variant		ENST00000324472.9	NP_776173.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPY19L2	ENST00000324472.9	c.804-7_804-5dupTTT		splice_region_variant, intron_variant		1	NM_173812.5	ENSP00000315988.4
DPY19L2	ENST00000306389.7	n.*287-7_*287-5dupTTT		splice_region_variant, intron_variant		1		ENSP00000445878.1
ENSG00000249753	ENST00000509615.2	n.239-2709_239-2707dupTTT		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 3042 AN: 127026 Hom.: 80 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00732

Gnomad AMI AF: 0.0315

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.0831

Gnomad SAS AF: 0.0127

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.00758

Gnomad NFE AF: 0.0316

Gnomad OTH AF: 0.0170

GnomAD3 exomes AF: 0.0228 AC: 2138 AN: 93570 Hom.: 210 AF XY: 0.0214 AC XY: 1110 AN XY: 51912

Gnomad AFR exome AF: 0.0264

Gnomad AMR exome AF: 0.0334

Gnomad ASJ exome AF: 0.0234

Gnomad EAS exome AF: 0.0601

Gnomad SAS exome AF: 0.0240

Gnomad FIN exome AF: 0.0124

Gnomad NFE exome AF: 0.0172

Gnomad OTH exome AF: 0.0279

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0263 AC: 30985 AN: 1178868 Hom.: 242 Cov.: 33 AF XY: 0.0262 AC XY: 15274 AN XY: 582806

Gnomad4 AFR exome AF: 0.0143

Gnomad4 AMR exome AF: 0.0253

Gnomad4 ASJ exome AF: 0.0277

Gnomad4 EAS exome AF: 0.0528

Gnomad4 SAS exome AF: 0.0324

Gnomad4 FIN exome AF: 0.0202

Gnomad4 NFE exome AF: 0.0257

Gnomad4 OTH exome AF: 0.0263

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0240 AC: 3043 AN: 127012 Hom.: 80 Cov.: 0 AF XY: 0.0229 AC XY: 1389 AN XY: 60610

Gnomad4 AFR AF: 0.00735

Gnomad4 AMR AF: 0.0147

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.0834

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0181

Gnomad4 NFE AF: 0.0316

Gnomad4 OTH AF: 0.0169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs371578418; hg19: chr12-64020310;