rs158584

Variant names:

• chr11-30964215-G-A
• rs158584
• NM_001387274.1:c.2592-11647C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-30964215-G-A
• chr11-30964215-G-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.2592-11647C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 152,210 control chromosomes in the GnomAD database, including 674 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 0.088 (674 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.2592-11647C>T		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.2592-11647C>T		intron_variant	Intron 20 of 38		NM_001387274.1	ENSP00000507427.1

Frequencies

GnomAD3 genomes AF: 0.0877 AC: 13331 AN: 152092 Hom.: 674 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.0876 AC: 13332 AN: 152210 Hom.: 674 Cov.: 32 AF XY: 0.0894 AC XY: 6656 AN XY: 74418

African (AFR) AF: 0.0448 AC: 1861 AN: 41556

American (AMR) AF: 0.108 AC: 1656 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3472

East Asian (EAS) AF: 0.138 AC: 714 AN: 5164

South Asian (SAS) AF: 0.108 AC: 522 AN: 4826

European-Finnish (FIN) AF: 0.0900 AC: 953 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0966 AC: 6570 AN: 68000

Other (OTH) AF: 0.117 AC: 248 AN: 2112

Alfa AF: 0.0839 Hom.: 357

Bravo AF: 0.0881

Asia WGS AF: 0.151 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.60
PhyloP100		0.48
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: rs158584; hg19: chr11-30985762;