11-30833358-T-G

Variant names:

• chr11-30833358-T-G
• rs1015541
• ENST00000444572.6:n.*410-1989A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663545.1(ENSG00000287373):​n.1154-14770T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,938 control chromosomes in the GnomAD database, including 29,314 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 0.61 (29314 hom., cov: 31)
• Consequence: ENSG00000287373 ENST00000663545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• 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]

ENSG00000287373 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663545.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	ENST00000444572.6	TSL:5	n.*410-1989A>C		intron	N/A	ENSP00000404672.2	H7C298
	ENSG00000287373	ENST00000663545.1		n.1154-14770T>G		intron	N/A
	ENSG00000287373	ENST00000749566.1		n.463+30016T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92676 AN: 151820 Hom.: 29306 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.610 AC: 92718 AN: 151938 Hom.: 29314 Cov.: 31 AF XY: 0.609 AC XY: 45232 AN XY: 74260

African (AFR) AF: 0.453 AC: 18777 AN: 41424

American (AMR) AF: 0.669 AC: 10211 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2836 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2376 AN: 5170

South Asian (SAS) AF: 0.669 AC: 3227 AN: 4826

European-Finnish (FIN) AF: 0.613 AC: 6475 AN: 10558

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46457 AN: 67926

Other (OTH) AF: 0.658 AC: 1388 AN: 2110

Alfa AF: 0.665 Hom.: 104754

Bravo AF: 0.607

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.68
PhyloP100		-0.62

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1015541;

hg19: chr11-30854905;