chr5-151206306-G-A

Variant names:

• chr5-151206306-G-A
• rs7724774
• NM_015621.3:c.49-831C>T

Variant summary

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

The NM_015621.3(CCDC69):​c.49-831C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 152,240 control chromosomes in the GnomAD database, including 677 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 0.085 (677 hom., cov: 31)
• Consequence: CCDC69 NM_015621.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 3 publications found

Genes affected

CCDC69 (HGNC:24487): (coiled-coil domain containing 69) Predicted to enable microtubule binding activity. Involved in spindle midzone assembly. Located in spindle midzone. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC69	NM_015621.3	c.49-831C>T		intron_variant	Intron 1 of 8	ENST00000355417.7	NP_056436.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC69	ENST00000355417.7	c.49-831C>T		intron_variant	Intron 1 of 8	1	NM_015621.3	ENSP00000347586.2
CCDC69	ENST00000521308.5	n.172-4618C>T		intron_variant	Intron 1 of 7	1
CCDC69	ENST00000522179.1	n.491-831C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12932 AN: 152122 Hom.: 673 Cov.: 31

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0850 AC: 12943 AN: 152240 Hom.: 677 Cov.: 31 AF XY: 0.0852 AC XY: 6341 AN XY: 74436

African (AFR) AF: 0.0221 AC: 919 AN: 41566

American (AMR) AF: 0.101 AC: 1542 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 344 AN: 3468

East Asian (EAS) AF: 0.0947 AC: 490 AN: 5174

South Asian (SAS) AF: 0.0815 AC: 393 AN: 4824

European-Finnish (FIN) AF: 0.0998 AC: 1059 AN: 10608

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7835 AN: 68000

Other (OTH) AF: 0.0985 AC: 208 AN: 2112

Alfa AF: 0.0575 Hom.: 94

Bravo AF: 0.0814

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.73
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7724774; hg19: chr5-150585867;