11-30878716-TAAAAAA-TAAAAAAAAAA

Variant names:

• chr11-30878716-T-TAAAA
• rs5790842
• NM_001387274.1:c.5234-9_5234-6dupTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001387274.1(DCDC1):​c.5234-9_5234-6dupTTTT variant causes a splice region, 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: not found (cov: 0)
  • Exomes 𝑓: 0.0000024 (0 hom.)
• Consequence: DCDC1 NM_001387274.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697
• Publications: 0 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]

ENSG00000287373 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387274.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	NM_001387274.1	MANE Select	c.5234-9_5234-6dupTTTT		splice_region intron	N/A	NP_001374203.1	A0A804HJA9
	DCDC1	NM_001367979.1		c.5225-9_5225-6dupTTTT		splice_region intron	N/A	NP_001354908.1	M0R2J8-1
	DCDC1	NM_020869.4		c.2546-9_2546-6dupTTTT		splice_region intron	N/A	NP_065920.2	B6ZDN3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	ENST00000684477.1	MANE Select	c.5234-6_5234-5insTTTT		splice_region intron	N/A	ENSP00000507427.1	A0A804HJA9
	DCDC1	ENST00000597505.5	TSL:5	c.5225-6_5225-5insTTTT		splice_region intron	N/A	ENSP00000472625.1	M0R2J8-1
	DCDC1	ENST00000406071.6	TSL:5	c.2546-6_2546-5insTTTT		splice_region intron	N/A	ENSP00000385936.3	B6ZDN3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000240 AC: 3 AN: 1250558 Hom.: 0 Cov.: 0 AF XY: 0.00000161 AC XY: 1 AN XY: 619936

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 26352

American (AMR) AF: 0.00 AC: 0 AN: 23916

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19474

East Asian (EAS) AF: 0.00 AC: 0 AN: 33828

South Asian (SAS) AF: 0.0000152 AC: 1 AN: 65638

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41178

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4394

European-Non Finnish (NFE) AF: 0.00000203 AC: 2 AN: 984410

Other (OTH) AF: 0.00 AC: 0 AN: 51368

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs5790842; hg19: chr11-30900263;