rs400964

chr11-31155713-T-Achr11-31155713-T-C

Variant summary

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

The NM_001387274.1(DCDC1):c.1222-17929A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,036 control chromosomes in the GnomAD database, including 25,202 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 0.57 (25202 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

Genes affected

DCDC1 (HGNC:20625): (doublecortin domain containing 1) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a hydrophilic, intracellular protein. It contains a single doublecortin domain and is unable to bind microtubules and to regulate microtubule polymerization. This gene is mainly expressed in adult testis. It does not have a mouse homolog. [provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC1	NM_001387274.1	c.1222-17929A>T		intron_variant		ENST00000684477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCDC1	ENST00000684477.1	c.1222-17929A>T		intron_variant			NM_001387274.1	A2
DCDC1	ENST00000597505.5	c.1222-17929A>T		intron_variant		5		A2
DCDC1	ENST00000342355.8	c.*297-17929A>T		intron_variant, NMD_transcript_variant		2
DCDC1	ENST00000534722.5	n.194-17929A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85922 AN: 151918 Hom.: 25196 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.565 AC: 85954 AN: 152036 Hom.: 25202 Cov.: 32 AF XY: 0.569 AC XY: 42255 AN XY: 74302

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.561

Alfa AF: 0.498 Hom.: 1585

Bravo AF: 0.552

Asia WGS AF: 0.797 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.7
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs400964; hg19: chr11-31177260;