chr10-80355863-T-C

Position:

• chr10-80355863-T-C

Variant summary

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

The NM_001269053.2(DYDC1):​c.-10+849A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 151,998 control chromosomes in the GnomAD database, including 44,862 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 0.76 (44862 hom., cov: 30)
• Consequence: DYDC1 NM_001269053.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

Genes affected

DYDC1 (HGNC:23460): (DPY30 domain containing 1) This gene encodes a member of a family of proteins that contains a DPY30 domain. The encoded protein is involved in acrosome formation during spermatid development. This gene locus overlaps with a closely related gene on the opposite strand. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

DYDC2 (HGNC:23468): (DPY30 domain containing 2) This gene encodes a member of a family of proteins that contains a DPY30 domain. This gene locus overlaps with a closely related gene on the opposite strand. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYDC1	NM_001269053.2	c.-10+849A>G		intron_variant		ENST00000372202.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYDC1	ENST00000372202.6	c.-10+849A>G		intron_variant		3	NM_001269053.2	P1

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115470 AN: 151882 Hom.: 44815 Cov.: 30

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.760 AC: 115576 AN: 151998 Hom.: 44862 Cov.: 30 AF XY: 0.765 AC XY: 56848 AN XY: 74272

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.749

Alfa AF: 0.717 Hom.: 5533

Bravo AF: 0.769

Asia WGS AF: 0.890 AC: 3094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.76

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: rs1340380; hg19: chr10-82115619;