rs1054174

Variant names:

• chr5-204837-C-T
• rs1054174
• NM_145265.3:c.*460G>A

Variant summary

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

The NM_145265.3(CCDC127):​c.*460G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,994 control chromosomes in the GnomAD database, including 10,905 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 (10869 hom., cov: 33)
  • Exomes 𝑓: 0.23 (36 hom.)
• Consequence: CCDC127 NM_145265.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516
• Publications: 17 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC127	NM_145265.3	c.*460G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000296824.4	NP_660308.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC127	ENST00000296824.4	c.*460G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_145265.3	ENSP00000296824.2

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52089 AN: 151960 Hom.: 10837 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.337

GnomAD4 exome AF: 0.226 AC: 207 AN: 916 Hom.: 36 Cov.: 0 AF XY: 0.228 AC XY: 102 AN XY: 448

African (AFR) AF: 0.618 AC: 21 AN: 34

American (AMR) AF: 0.227 AC: 5 AN: 22

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 6 AN: 22

East Asian (EAS) AF: 0.125 AC: 2 AN: 16

South Asian (SAS) AF: 0.0556 AC: 1 AN: 18

European-Finnish (FIN) AF: 0.326 AC: 15 AN: 46

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.202 AC: 143 AN: 708

Other (OTH) AF: 0.280 AC: 14 AN: 50

GnomAD4 genome AF: 0.343 AC: 52170 AN: 152078 Hom.: 10869 Cov.: 33 AF XY: 0.339 AC XY: 25193 AN XY: 74340

African (AFR) AF: 0.583 AC: 24179 AN: 41458

American (AMR) AF: 0.325 AC: 4966 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3468

East Asian (EAS) AF: 0.0563 AC: 291 AN: 5168

South Asian (SAS) AF: 0.161 AC: 775 AN: 4826

European-Finnish (FIN) AF: 0.280 AC: 2958 AN: 10578

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16959 AN: 67980

Other (OTH) AF: 0.333 AC: 703 AN: 2112

Alfa AF: 0.275 Hom.: 12782

Bravo AF: 0.360

Asia WGS AF: 0.144 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.62
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1054174; hg19: chr5-204952;