rs514207

Variant names:

• chr11-31057572-G-A
• rs514207
• NM_001387274.1:c.2591+6897C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-31057572-G-A
• chr11-31057572-G-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.2591+6897C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,006 control chromosomes in the GnomAD database, including 1,398 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 0.13 (1398 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.2591+6897C>T		intron_variant	Intron 20 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.2591+6897C>T		intron_variant	Intron 20 of 38		NM_001387274.1	ENSP00000507427.1
DCDC1	ENST00000597505.5	c.2591+6897C>T		intron_variant	Intron 18 of 35	5		ENSP00000472625.1
DCDC1	ENST00000342355.8	n.*1666+6897C>T		intron_variant	Intron 20 of 21	2		ENSP00000343496.4
DCDC1	ENST00000437348.5	n.1299+6897C>T		intron_variant	Intron 10 of 11	5

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19014 AN: 151888 Hom.: 1399 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0791

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.125 AC: 19034 AN: 152006 Hom.: 1398 Cov.: 32 AF XY: 0.126 AC XY: 9363 AN XY: 74294

African (AFR) AF: 0.177 AC: 7330 AN: 41442

American (AMR) AF: 0.163 AC: 2494 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0791 AC: 274 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1480 AN: 5150

South Asian (SAS) AF: 0.160 AC: 772 AN: 4820

European-Finnish (FIN) AF: 0.0743 AC: 786 AN: 10582

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0805 AC: 5474 AN: 67972

Other (OTH) AF: 0.120 AC: 253 AN: 2110

Alfa AF: 0.0987 Hom.: 163

Bravo AF: 0.139

Asia WGS AF: 0.238 AC: 826 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.65
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: rs514207; hg19: chr11-31079119;