NM_001387274.1:c.4710G>A

Variant names:

• chr11-30899596-C-T
• rs7947732
• NM_001387274.1:c.4710G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Moderate BP6 BP7 BA1

The NM_001387274.1(DCDC1):​c.4710G>A​(p.Lys1570Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00373 in 1,578,370 control chromosomes in the GnomAD database, including 176 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.018 (86 hom., cov: 32)
  • Exomes 𝑓: 0.0022 (90 hom.)
• Consequence: DCDC1 NM_001387274.1 synonymous
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 1.59
• Publications: 2 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]

ENSG00000287373 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.035).
• BP6: Variant 11-30899596-C-T is Benign according to our data. Variant chr11-30899596-C-T is described in ClinVar as Benign. ClinVar VariationId is 3352623.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP7: Synonymous conserved (PhyloP=1.59 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0604 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.4710G>A	p.Lys1570Lys	synonymous	Exon 34 of 39	NP_001374203.1	A0A804HJA9
	DCDC1	NM_001367979.1		c.4701G>A	p.Lys1567Lys	synonymous	Exon 34 of 39	NP_001354908.1	M0R2J8-1
	DCDC1	NM_020869.4		c.2022G>A	p.Lys674Lys	synonymous	Exon 15 of 20	NP_065920.2	B6ZDN3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	ENST00000684477.1	MANE Select	c.4710G>A	p.Lys1570Lys	synonymous	Exon 34 of 39	ENSP00000507427.1	A0A804HJA9
	DCDC1	ENST00000597505.5	TSL:5	c.4701G>A	p.Lys1567Lys	synonymous	Exon 32 of 36	ENSP00000472625.1	M0R2J8-1
	DCDC1	ENST00000406071.6	TSL:5	c.2022G>A	p.Lys674Lys	synonymous	Exon 15 of 20	ENSP00000385936.3	B6ZDN3

Frequencies

GnomAD3 genomes AF: 0.0181 AC: 2753 AN: 151976 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00616

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00829

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.0120

GnomAD2 exomes AF: 0.00515 AC: 1127 AN: 219046 AF XY: 0.00418

Gnomad AFR exome AF: 0.0573

Gnomad AMR exome AF: 0.00324

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000187

Gnomad OTH exome AF: 0.00203

GnomAD4 exome AF: 0.00219 AC: 3129 AN: 1426276 Hom.: 90 Cov.: 30 AF XY: 0.00222 AC XY: 1569 AN XY: 707450

African (AFR) AF: 0.0632 AC: 2054 AN: 32490

American (AMR) AF: 0.00349 AC: 143 AN: 40928

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25346

East Asian (EAS) AF: 0.00 AC: 0 AN: 38856

South Asian (SAS) AF: 0.00695 AC: 548 AN: 78862

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51766

Middle Eastern (MID) AF: 0.00142 AC: 8 AN: 5652

European-Non Finnish (NFE) AF: 0.0000631 AC: 69 AN: 1093542

Other (OTH) AF: 0.00522 AC: 307 AN: 58834

GnomAD4 genome AF: 0.0181 AC: 2759 AN: 152094 Hom.: 86 Cov.: 32 AF XY: 0.0177 AC XY: 1319 AN XY: 74358

African (AFR) AF: 0.0624 AC: 2589 AN: 41508

American (AMR) AF: 0.00615 AC: 94 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.00830 AC: 40 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10600

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000147 AC: 10 AN: 67932

Other (OTH) AF: 0.0118 AC: 25 AN: 2114

Alfa AF: 0.00970 Hom.: 55

Bravo AF: 0.0205

Asia WGS AF: 0.00927 AC: 32 AN: 3468

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	DCDC5-related condition (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Pathogenic	0.16
CADD	Benign	2.1
DANN	Benign	0.95
PhyloP100		1.6
Mutation Taster		=91/9	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7947732; hg19: chr11-30921143;