chr11-30878716-TA-T

Variant names:

• chr11-30878716-TA-T
• rs5790842
• NM_001387274.1:c.5234-6delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001387274.1(DCDC1):​c.5234-6delT 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: 𝑓 0.47 (16010 hom., cov: 0)
  • Exomes 𝑓: 0.46 (5767 hom.)
  • Failed GnomAD Quality Control
• Consequence: DCDC1 NM_001387274.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697
• Publications: 1 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

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.5234-6delT		splice_region intron	N/A	NP_001374203.1	A0A804HJA9
	DCDC1	NM_001367979.1		c.5225-6delT		splice_region intron	N/A	NP_001354908.1	M0R2J8-1
	DCDC1	NM_020869.4		c.2546-6delT		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.5234-6delT		splice_region intron	N/A	ENSP00000507427.1	A0A804HJA9
	DCDC1	ENST00000597505.5	TSL:5	c.5225-6delT		splice_region intron	N/A	ENSP00000472625.1	M0R2J8-1
	DCDC1	ENST00000406071.6	TSL:5	c.2546-6delT		splice_region intron	N/A	ENSP00000385936.3	B6ZDN3

Frequencies

GnomAD3 genomes AF: 0.468 AC: 65530 AN: 140034 Hom.: 16011 Cov.: 0

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.498

GnomAD2 exomes AF: 0.468 AC: 53674 AN: 114698 AF XY: 0.468

Gnomad AFR exome AF: 0.422

Gnomad AMR exome AF: 0.449

Gnomad ASJ exome AF: 0.464

Gnomad EAS exome AF: 0.452

Gnomad FIN exome AF: 0.484

Gnomad NFE exome AF: 0.480

Gnomad OTH exome AF: 0.475

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.457 AC: 555550 AN: 1215402 Hom.: 5767 Cov.: 0 AF XY: 0.457 AC XY: 275490 AN XY: 603222

African (AFR) AF: 0.379 AC: 9319 AN: 24582

American (AMR) AF: 0.412 AC: 9642 AN: 23424

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 8829 AN: 19194

East Asian (EAS) AF: 0.432 AC: 14011 AN: 32396

South Asian (SAS) AF: 0.432 AC: 27867 AN: 64446

European-Finnish (FIN) AF: 0.439 AC: 17696 AN: 40284

Middle Eastern (MID) AF: 0.462 AC: 2002 AN: 4338

European-Non Finnish (NFE) AF: 0.464 AC: 443639 AN: 956804

Other (OTH) AF: 0.451 AC: 22545 AN: 49934

GnomAD4 genome AF: 0.468 AC: 65538 AN: 140082 Hom.: 16010 Cov.: 0 AF XY: 0.463 AC XY: 31380 AN XY: 67774

African (AFR) AF: 0.257 AC: 9596 AN: 37342

American (AMR) AF: 0.467 AC: 6526 AN: 13964

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2167 AN: 3378

East Asian (EAS) AF: 0.315 AC: 1496 AN: 4750

South Asian (SAS) AF: 0.536 AC: 2331 AN: 4352

European-Finnish (FIN) AF: 0.479 AC: 3933 AN: 8218

Middle Eastern (MID) AF: 0.592 AC: 161 AN: 272

European-Non Finnish (NFE) AF: 0.582 AC: 37842 AN: 65016

Other (OTH) AF: 0.503 AC: 962 AN: 1914

Alfa AF: 0.275 Hom.: 578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.70
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: rs5790842; hg19: chr11-30900263; COSMIC: COSV57997261;