chr11-124951679-T-A

Variant names:

• chr11-124951679-T-A
• rs4408325
• ENST00000649496.2:n.511-129A>T

Variant summary

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

The ENST00000649496.2(CCDC15-DT):​n.511-129A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,000 control chromosomes in the GnomAD database, including 39,207 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 0.71 (39207 hom., cov: 30)
• Consequence: CCDC15-DT ENST00000649496.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 10 publications found

Genes affected

CCDC15-DT (HGNC:54193): (CCDC15 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC15-DT	XR_948132.3	n.511-129A>T		intron_variant	Intron 1 of 2
CCDC15-DT	XR_948133.3	n.511-129A>T		intron_variant	Intron 1 of 2
CCDC15-DT	XR_948134.3	n.511-129A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC15-DT	ENST00000649496.2	n.511-129A>T		intron_variant	Intron 1 of 2
CCDC15-DT	ENST00000655771.2	n.564-129A>T		intron_variant	Intron 1 of 2
CCDC15-DT	ENST00000667169.2	n.48-129A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107713 AN: 151882 Hom.: 39156 Cov.: 30

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.709 AC: 107825 AN: 152000 Hom.: 39207 Cov.: 30 AF XY: 0.713 AC XY: 52997 AN XY: 74282

African (AFR) AF: 0.840 AC: 34823 AN: 41464

American (AMR) AF: 0.656 AC: 10036 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2879 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4803 AN: 5166

South Asian (SAS) AF: 0.848 AC: 4063 AN: 4794

European-Finnish (FIN) AF: 0.637 AC: 6727 AN: 10558

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42146 AN: 67940

Other (OTH) AF: 0.720 AC: 1520 AN: 2110

Alfa AF: 0.512 Hom.: 1247

Bravo AF: 0.715

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.50
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4408325; hg19: chr11-124821575;