rs248450

Variant names:

• chr5-151197206-G-A
• rs248450
• NM_015621.3:c.319+1791C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-151197206-G-A
• chr5-151197206-G-C

Variant summary

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

The NM_015621.3(CCDC69):​c.319+1791C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,074 control chromosomes in the GnomAD database, including 28,142 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 0.60 (28142 hom., cov: 32)
• Consequence: CCDC69 NM_015621.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC69	NM_015621.3	c.319+1791C>T		intron_variant	Intron 4 of 8	ENST00000355417.7	NP_056436.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC69	ENST00000355417.7	c.319+1791C>T		intron_variant	Intron 4 of 8	1	NM_015621.3	ENSP00000347586.2
CCDC69	ENST00000518189.5	n.271+1791C>T		intron_variant	Intron 3 of 7	1		ENSP00000430549.1
CCDC69	ENST00000521308.5	n.366+1791C>T		intron_variant	Intron 3 of 7	1
CCDC69	ENST00000522964.1	n.183+4376C>T		intron_variant	Intron 2 of 4	5		ENSP00000428588.1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91052 AN: 151956 Hom.: 28109 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.599 AC: 91127 AN: 152074 Hom.: 28142 Cov.: 32 AF XY: 0.598 AC XY: 44439 AN XY: 74320

African (AFR) AF: 0.484 AC: 20069 AN: 41474

American (AMR) AF: 0.682 AC: 10423 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2227 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1449 AN: 5168

South Asian (SAS) AF: 0.484 AC: 2333 AN: 4822

European-Finnish (FIN) AF: 0.677 AC: 7155 AN: 10566

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45331 AN: 67988

Other (OTH) AF: 0.643 AC: 1359 AN: 2114

Alfa AF: 0.644 Hom.: 132813

Bravo AF: 0.594

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.68
PhyloP100		0.38
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: rs248450; hg19: chr5-150576767;