rs12577026

Variant names:

• chr11-31326296-G-A
• rs12577026
• NM_001387274.1:c.164+1821C>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.164+1821C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,978 control chromosomes in the GnomAD database, including 2,131 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 0.15 (2131 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• 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 (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.164+1821C>T		intron_variant	Intron 3 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.164+1821C>T		intron_variant	Intron 3 of 38		NM_001387274.1	ENSP00000507427.1
DCDC1	ENST00000452803.1	c.164+1821C>T		intron_variant	Intron 3 of 8	1		ENSP00000389792.1
DCDC1	ENST00000597505.5	c.164+1821C>T		intron_variant	Intron 1 of 35	5		ENSP00000472625.1
DCDC1	ENST00000342355.8	n.164+1821C>T		intron_variant	Intron 3 of 21	2		ENSP00000343496.4

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22496 AN: 151860 Hom.: 2119 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.148 AC: 22512 AN: 151978 Hom.: 2131 Cov.: 32 AF XY: 0.143 AC XY: 10617 AN XY: 74282

African (AFR) AF: 0.0374 AC: 1554 AN: 41512

American (AMR) AF: 0.146 AC: 2228 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 753 AN: 3462

East Asian (EAS) AF: 0.206 AC: 1067 AN: 5170

South Asian (SAS) AF: 0.143 AC: 688 AN: 4818

European-Finnish (FIN) AF: 0.108 AC: 1134 AN: 10532

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14391 AN: 67906

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.178 Hom.: 322

Bravo AF: 0.145

Asia WGS AF: 0.195 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.69
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12577026; hg19: chr11-31347843;