11-30871277-A-G

Variant names:

• chr11-30871277-A-G
• rs1448938
• NM_001387274.1:c.*41-5945T>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.*41-5945T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,928 control chromosomes in the GnomAD database, including 18,377 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 0.47 (18377 hom., cov: 31)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 15 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 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.*41-5945T>C		intron	N/A	NP_001374203.1	A0A804HJA9
	DCDC1	NM_001367979.1		c.*41-5945T>C		intron	N/A	NP_001354908.1	M0R2J8-1
	DCDC1	NM_020869.4		c.*41-5945T>C		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.*41-5945T>C		intron	N/A	ENSP00000507427.1	A0A804HJA9
	DCDC1	ENST00000406071.6	TSL:5	c.*41-5945T>C		intron	N/A	ENSP00000385936.3	B6ZDN3
	DCDC1	ENST00000303697.8	TSL:2	n.*1718-5945T>C		intron	N/A	ENSP00000306898.4	H0Y2Q8

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71800 AN: 151810 Hom.: 18367 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.473 AC: 71837 AN: 151928 Hom.: 18377 Cov.: 31 AF XY: 0.468 AC XY: 34742 AN XY: 74252

African (AFR) AF: 0.286 AC: 11865 AN: 41442

American (AMR) AF: 0.459 AC: 7008 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2251 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1561 AN: 5136

South Asian (SAS) AF: 0.531 AC: 2558 AN: 4816

European-Finnish (FIN) AF: 0.486 AC: 5121 AN: 10542

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39689 AN: 67950

Other (OTH) AF: 0.509 AC: 1073 AN: 2110

Alfa AF: 0.427 Hom.: 2051

Bravo AF: 0.460

Asia WGS AF: 0.413 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.8
DANN	Benign	0.81
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs1448938; hg19: chr11-30892824;