rs1208134

Variant names:

• chr1-169459706-C-A
• ENST00000545005.5:c.-24+91G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-169459706-C-A
• chr1-169459706-C-G
• chr1-169459706-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001300968.1(CCDC181):​c.-24+91G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 27)
• Consequence: CCDC181 NM_001300968.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

CCDC181 (HGNC:28051): (coiled-coil domain containing 181) Predicted to enable microtubule binding activity. Predicted to be located in manchette and sperm flagellum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC181	NM_001300968.1	c.-24+91G>T		intron_variant	Intron 2 of 6		NP_001287897.1
CCDC181	XM_005245383.1	c.-24+91G>T		intron_variant	Intron 2 of 6		XP_005245440.1
CCDC181	XM_017001938.2	c.-105+91G>T		intron_variant	Intron 2 of 7		XP_016857427.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC181	ENST00000545005.5	c.-24+91G>T		intron_variant	Intron 2 of 6	1		ENSP00000442297.1
CCDC181	ENST00000445428.5	n.268+91G>T		intron_variant	Intron 2 of 5	1
CCDC181	ENST00000437857.2	n.237+91G>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes Cov.: 27

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

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.44

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-169428944;