rs1547131

Variant names:

• chr11-31365052-A-G
• rs1547131
• NM_001387274.1:c.-125+4645T>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.-125+4645T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,012 control chromosomes in the GnomAD database, including 6,414 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 0.29 (6414 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• 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 = 0.321 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.-125+4645T>C		intron	N/A	NP_001374203.1	A0A804HJA9
	DCDC1	NM_001367979.1		c.-125+4645T>C		intron	N/A	NP_001354908.1	M0R2J8-1
	DCDC1	NM_181807.4		c.-125+4645T>C		intron	N/A	NP_861523.2	M0R2J8-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	ENST00000684477.1	MANE Select	c.-125+4645T>C		intron	N/A	ENSP00000507427.1	A0A804HJA9
	DCDC1	ENST00000452803.1	TSL:1	c.-125+4645T>C		intron	N/A	ENSP00000389792.1	M0R2J8-3
	DCDC1	ENST00000342355.8	TSL:2	n.-125+4645T>C		intron	N/A	ENSP00000343496.4	M0R2J8-2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43686 AN: 151894 Hom.: 6406 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.288 AC: 43718 AN: 152012 Hom.: 6414 Cov.: 32 AF XY: 0.281 AC XY: 20873 AN XY: 74310

African (AFR) AF: 0.326 AC: 13502 AN: 41454

American (AMR) AF: 0.281 AC: 4297 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1532 AN: 5144

South Asian (SAS) AF: 0.290 AC: 1397 AN: 4814

European-Finnish (FIN) AF: 0.140 AC: 1478 AN: 10588

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19393 AN: 67958

Other (OTH) AF: 0.306 AC: 645 AN: 2110

Alfa AF: 0.283 Hom.: 790

Bravo AF: 0.298

Asia WGS AF: 0.339 AC: 1175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.99
DANN	Benign	0.38
PhyloP100		-0.31
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: rs1547131; hg19: chr11-31386599;