11-31092650-G-T

Variant names:

• chr11-31092650-G-T
• rs621549
• NM_001387274.1:c.2119-1139C>A

Variant summary

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

The NM_001387274.1(DCDC1):​c.2119-1139C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,022 control chromosomes in the GnomAD database, including 18,402 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 0.49 (18402 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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.2119-1139C>A		intron	N/A	NP_001374203.1	A0A804HJA9
	DCDC1	NM_001367979.1		c.2119-1139C>A		intron	N/A	NP_001354908.1	M0R2J8-1
	DCDC1	NR_170625.1		n.2174-1139C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	ENST00000684477.1	MANE Select	c.2119-1139C>A		intron	N/A	ENSP00000507427.1	A0A804HJA9
	DCDC1	ENST00000597505.5	TSL:5	c.2119-1139C>A		intron	N/A	ENSP00000472625.1	M0R2J8-1
	DCDC1	ENST00000342355.8	TSL:2	n.*1194-1139C>A		intron	N/A	ENSP00000343496.4	M0R2J8-2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74193 AN: 151902 Hom.: 18369 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.489 AC: 74274 AN: 152022 Hom.: 18402 Cov.: 32 AF XY: 0.488 AC XY: 36214 AN XY: 74272

African (AFR) AF: 0.567 AC: 23534 AN: 41476

American (AMR) AF: 0.500 AC: 7639 AN: 15280

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

East Asian (EAS) AF: 0.332 AC: 1716 AN: 5174

South Asian (SAS) AF: 0.451 AC: 2175 AN: 4822

European-Finnish (FIN) AF: 0.472 AC: 4976 AN: 10544

Middle Eastern (MID) AF: 0.576 AC: 167 AN: 290

European-Non Finnish (NFE) AF: 0.450 AC: 30575 AN: 67938

Other (OTH) AF: 0.510 AC: 1078 AN: 2114

Alfa AF: 0.320 Hom.: 800

Bravo AF: 0.498

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.28
PhyloP100		0.77
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: rs621549; hg19: chr11-31114197;