5-204962-G-C

Variant names:

• chr5-204962-G-C
• rs13474
• NM_145265.3:c.*335C>G

Variant summary

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

The NM_145265.3(CCDC127):​c.*335C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 192,050 control chromosomes in the GnomAD database, including 4,946 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 0.20 (4503 hom., cov: 33)
  • Exomes 𝑓: 0.12 (443 hom.)
• Consequence: CCDC127 NM_145265.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 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.*335C>G		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.*335C>G		3_prime_UTR	Exon 3 of 3	ENSP00000296824.2	Q96BQ5
	CCDC127	ENST00000918339.1		c.*335C>G		3_prime_UTR	Exon 3 of 3	ENSP00000588398.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31072 AN: 152032 Hom.: 4492 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.000960

Gnomad SAS AF: 0.0755

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.122 AC: 4874 AN: 39900 Hom.: 443 Cov.: 0 AF XY: 0.121 AC XY: 2435 AN XY: 20094

African (AFR) AF: 0.392 AC: 631 AN: 1610

American (AMR) AF: 0.148 AC: 186 AN: 1254

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 173 AN: 1716

East Asian (EAS) AF: 0.00 AC: 0 AN: 2852

South Asian (SAS) AF: 0.0462 AC: 24 AN: 520

European-Finnish (FIN) AF: 0.178 AC: 318 AN: 1782

Middle Eastern (MID) AF: 0.0885 AC: 23 AN: 260

European-Non Finnish (NFE) AF: 0.116 AC: 3147 AN: 27216

Other (OTH) AF: 0.138 AC: 372 AN: 2690

GnomAD4 genome AF: 0.205 AC: 31117 AN: 152150 Hom.: 4503 Cov.: 33 AF XY: 0.203 AC XY: 15079 AN XY: 74402

African (AFR) AF: 0.403 AC: 16727 AN: 41470

American (AMR) AF: 0.153 AC: 2347 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3468

East Asian (EAS) AF: 0.000962 AC: 5 AN: 5196

South Asian (SAS) AF: 0.0756 AC: 365 AN: 4828

European-Finnish (FIN) AF: 0.197 AC: 2076 AN: 10564

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8700 AN: 68008

Other (OTH) AF: 0.183 AC: 388 AN: 2116

Alfa AF: 0.0870 Hom.: 152

Bravo AF: 0.210

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-0.71
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: rs13474; hg19: chr5-205077;