NM_001144981.3:c.315+9419A>G

Variant names:

• chr13-36274050-T-C
• rs912927
• NM_001144981.3:c.315+9419A>G

Variant summary

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

The NM_001144981.3(CCDC169):​c.315+9419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,092 control chromosomes in the GnomAD database, including 5,213 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 0.25 (5213 hom., cov: 32)
• Consequence: CCDC169 NM_001144981.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 13 publications found

Genes affected

CCDC169 (HGNC:34361): (coiled-coil domain containing 169)

CCDC169-SOHLH2 (HGNC:38866): (CCDC169-SOHLH2 readthrough) This locus represents naturally occurring read-through transcription between the neighboring C13orf38 (chromosome 13 open reading frame 38) and SOHLH2 (spermatogenesis and oogenesis specific basic helix-loop-helix 2) genes. The read-through transcript encodes a fusion protein that shares sequence identity with the products of each individual gene. [provided by RefSeq, Nov 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144981.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC169	NM_001144981.3	MANE Select	c.315+9419A>G		intron	N/A	NP_001138453.1
	CCDC169-SOHLH2	NM_001198910.2		c.15+9542A>G		intron	N/A	NP_001185839.1
	CCDC169	NM_001198908.2		c.315+9419A>G		intron	N/A	NP_001185837.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC169	ENST00000239859.8	TSL:5 MANE Select	c.315+9419A>G		intron	N/A	ENSP00000239859.7
	CCDC169-SOHLH2	ENST00000511166.1	TSL:2	c.15+9542A>G		intron	N/A	ENSP00000421868.1
	CCDC169	ENST00000503173.5	TSL:1	c.315+9419A>G		intron	N/A	ENSP00000426174.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38693 AN: 151974 Hom.: 5217 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.255 AC: 38724 AN: 152092 Hom.: 5213 Cov.: 32 AF XY: 0.256 AC XY: 19015 AN XY: 74330

African (AFR) AF: 0.190 AC: 7876 AN: 41480

American (AMR) AF: 0.298 AC: 4546 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3468

East Asian (EAS) AF: 0.488 AC: 2514 AN: 5148

South Asian (SAS) AF: 0.279 AC: 1342 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2292 AN: 10590

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18582 AN: 67998

Other (OTH) AF: 0.228 AC: 481 AN: 2112

Alfa AF: 0.261 Hom.: 7384

Bravo AF: 0.255

Asia WGS AF: 0.389 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.99
DANN	Benign	0.78
PhyloP100		-0.52
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: rs912927; hg19: chr13-36848187; COSMIC: COSV53484417;