11-31189224-G-A

Variant names:

• chr11-31189224-G-A
• rs16921914
• NM_001387274.1:c.1222-51440C>T

Variant summary

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

The NM_001387274.1(DCDC1):​c.1222-51440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,002 control chromosomes in the GnomAD database, including 4,732 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 0.22 (4732 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607
• Publications: 26 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	NM_001387274.1	MANE Select	c.1222-51440C>T		intron	N/A	NP_001374203.1
	DCDC1	NM_001367979.1		c.1222-51440C>T		intron	N/A	NP_001354908.1
	DCDC1	NR_170625.1		n.1276+25946C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	ENST00000684477.1	MANE Select	c.1222-51440C>T		intron	N/A	ENSP00000507427.1
	DCDC1	ENST00000597505.5	TSL:5	c.1222-51440C>T		intron	N/A	ENSP00000472625.1
	DCDC1	ENST00000342355.8	TSL:2	n.*296+25946C>T		intron	N/A	ENSP00000343496.4

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33726 AN: 151884 Hom.: 4735 Cov.: 32

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.222 AC: 33720 AN: 152002 Hom.: 4732 Cov.: 32 AF XY: 0.229 AC XY: 17003 AN XY: 74282

African (AFR) AF: 0.0565 AC: 2344 AN: 41496

American (AMR) AF: 0.234 AC: 3573 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2001 AN: 5150

South Asian (SAS) AF: 0.282 AC: 1351 AN: 4798

European-Finnish (FIN) AF: 0.387 AC: 4079 AN: 10548

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19182 AN: 67960

Other (OTH) AF: 0.196 AC: 415 AN: 2112

Alfa AF: 0.255 Hom.: 22598

Bravo AF: 0.201

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.2
DANN	Benign	0.71
PhyloP100		0.61
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: rs16921914; hg19: chr11-31210771;