rs288463

Variant names:

• chr11-31042354-T-G
• rs288463
• NM_001387274.1:c.2591+22115A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387274.1(DCDC1):​c.2591+22115A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,012 control chromosomes in the GnomAD database, including 20,767 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 0.51 (20767 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.2591+22115A>C		intron_variant	Intron 20 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.2591+22115A>C		intron_variant	Intron 20 of 38		NM_001387274.1	ENSP00000507427.1
DCDC1	ENST00000597505.5	c.2591+22115A>C		intron_variant	Intron 18 of 35	5		ENSP00000472625.1
DCDC1	ENST00000342355.8	n.*1666+22115A>C		intron_variant	Intron 20 of 21	2		ENSP00000343496.4
DCDC1	ENST00000437348.5	n.1299+22115A>C		intron_variant	Intron 10 of 11	5

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78103 AN: 151894 Hom.: 20734 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.514 AC: 78186 AN: 152012 Hom.: 20767 Cov.: 32 AF XY: 0.512 AC XY: 38048 AN XY: 74306

African (AFR) AF: 0.655 AC: 27169 AN: 41458

American (AMR) AF: 0.513 AC: 7828 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1884 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1718 AN: 5182

South Asian (SAS) AF: 0.455 AC: 2192 AN: 4814

European-Finnish (FIN) AF: 0.472 AC: 4985 AN: 10558

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.450 AC: 30598 AN: 67944

Other (OTH) AF: 0.529 AC: 1117 AN: 2112

Alfa AF: 0.476 Hom.: 67413

Bravo AF: 0.529

Asia WGS AF: 0.410 AC: 1425 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.76
PhyloP100		0.0020
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs288463; hg19: chr11-31063901;