12-63626530-TA-TAAAAAAA

Position:

• chr12-63626530-TA-TAAAAAAA

Variant summary

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

The NM_173812.5(DPY19L2):​c.804-5_804-4insTTTTTT variant causes a splice region, splice polypyrimidine tract, 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 0.0000079 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00016 (3 hom.)
  • Failed GnomAD Quality Control
• Consequence: DPY19L2 NM_173812.5 splice_region, splice_polypyrimidine_tract, 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]

(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.804-5_804-4insTTTTTT		splice_region_variant, splice_polypyrimidine_tract_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.804-5_804-4insTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_173812.5	ENSP00000315988	P1
DPY19L2	ENST00000306389.7	c.*287-5_*287-4insTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		1		ENSP00000445878
	ENST00000509615.2	n.239-2707_239-2706insTTTTTT		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00000785 AC: 1 AN: 127324 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000231

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000930 AC: 87 AN: 93570 Hom.: 8 AF XY: 0.000867 AC XY: 45 AN XY: 51912

Gnomad AFR exome AF: 0.00154

Gnomad AMR exome AF: 0.00160

Gnomad ASJ exome AF: 0.000710

Gnomad EAS exome AF: 0.00362

Gnomad SAS exome AF: 0.000244

Gnomad FIN exome AF: 0.000277

Gnomad NFE exome AF: 0.000719

Gnomad OTH exome AF: 0.00129

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000162 AC: 198 AN: 1219792 Hom.: 3 Cov.: 33 AF XY: 0.000187 AC XY: 113 AN XY: 603326

Gnomad4 AFR exome AF: 0.000120

Gnomad4 AMR exome AF: 0.000489

Gnomad4 ASJ exome AF: 0.000303

Gnomad4 EAS exome AF: 0.000830

Gnomad4 SAS exome AF: 0.000557

Gnomad4 FIN exome AF: 0.000249

Gnomad4 NFE exome AF: 0.000106

Gnomad4 OTH exome AF: 0.000121

GnomAD4 genome AF: 0.00000785 AC: 1 AN: 127324 Hom.: 0 Cov.: 0 AF XY: 0.0000165 AC XY: 1 AN XY: 60746

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000231

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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;