rs9312960

Variant names:

• chr5-203967-C-A
• rs9312960
• NM_145265.3:c.*1330G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-203967-C-A
• chr5-203967-C-T

Variant summary

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

The NM_145265.3(CCDC127):​c.*1330G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,044 control chromosomes in the GnomAD database, including 10,264 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 0.34 (10263 hom., cov: 33)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: CCDC127 NM_145265.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 14 publications found

Genes affected

CCDC127 (HGNC:30520): (coiled-coil domain containing 127) Predicted to be integral component of membrane. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145265.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC127	NM_145265.3	MANE Select	c.*1330G>T		3_prime_UTR	Exon 3 of 3	NP_660308.1	Q96BQ5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC127	ENST00000296824.4	TSL:1 MANE Select	c.*1330G>T		3_prime_UTR	Exon 3 of 3	ENSP00000296824.2	Q96BQ5

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50925 AN: 151890 Hom.: 10236 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0570

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.306 AC: 11 AN: 36 Hom.: 1 Cov.: 0 AF XY: 0.292 AC XY: 7 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.667 AC: 4 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.227 AC: 5 AN: 22

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.335 AC: 50998 AN: 152008 Hom.: 10263 Cov.: 33 AF XY: 0.331 AC XY: 24627 AN XY: 74308

African (AFR) AF: 0.558 AC: 23124 AN: 41444

American (AMR) AF: 0.323 AC: 4936 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3470

East Asian (EAS) AF: 0.0565 AC: 293 AN: 5184

South Asian (SAS) AF: 0.161 AC: 776 AN: 4822

European-Finnish (FIN) AF: 0.279 AC: 2943 AN: 10554

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16880 AN: 67942

Other (OTH) AF: 0.330 AC: 698 AN: 2114

Alfa AF: 0.275 Hom.: 18073

Bravo AF: 0.352

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.18
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: rs9312960; hg19: chr5-204082;