11-30871277-A-G

Position:

• chr11-30871277-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC124902656 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.*41-5945T>C		intron_variant		ENST00000684477.1	NP_001374203.1
LOC124902656	XR_007062643.1	n.493+1220A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.*41-5945T>C		intron_variant			NM_001387274.1	ENSP00000507427	A2

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

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.509

Alfa AF: 0.433 Hom.: 2028

Bravo AF: 0.460

Asia WGS AF: 0.413 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448938; hg19: chr11-30892824;