rs560395

Variant names:

• chr11-31066246-A-G
• rs560395
• NM_001387274.1:c.2299-1093T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-31066246-A-G
• chr11-31066246-A-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.2299-1093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,086 control chromosomes in the GnomAD database, including 23,349 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 0.54 (23349 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.2299-1093T>C		intron_variant	Intron 18 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.2299-1093T>C		intron_variant	Intron 18 of 38		NM_001387274.1	ENSP00000507427.1
DCDC1	ENST00000597505.5	c.2299-1093T>C		intron_variant	Intron 16 of 35	5		ENSP00000472625.1
DCDC1	ENST00000342355.8	n.*1374-1093T>C		intron_variant	Intron 18 of 21	2		ENSP00000343496.4
DCDC1	ENST00000437348.5	n.1007-1093T>C		intron_variant	Intron 8 of 11	5

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81877 AN: 151968 Hom.: 23315 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.539 AC: 81963 AN: 152086 Hom.: 23349 Cov.: 32 AF XY: 0.536 AC XY: 39840 AN XY: 74338

African (AFR) AF: 0.738 AC: 30652 AN: 41506

American (AMR) AF: 0.521 AC: 7954 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1884 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1716 AN: 5166

South Asian (SAS) AF: 0.477 AC: 2300 AN: 4824

European-Finnish (FIN) AF: 0.471 AC: 4976 AN: 10558

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30632 AN: 67974

Other (OTH) AF: 0.544 AC: 1150 AN: 2114

Alfa AF: 0.524 Hom.: 4086

Bravo AF: 0.556

Asia WGS AF: 0.426 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.94
DANN	Benign	0.37
PhyloP100		-0.49
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: rs560395; hg19: chr11-31087793;