rs1128226

Positions:

• chr7-21902051-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018719.5(CDCA7L):​c.*271T>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 0.341 in 468,818 control chromosomes in the GnomAD database, including 28,511 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 (8858 hom., cov: 34)
  • Exomes 𝑓: 0.34 (19653 hom.)
• Consequence: CDCA7L NM_018719.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

CDCA7L (HGNC:30777): (cell division cycle associated 7 like) Acts upstream of or within positive regulation of cell population proliferation. Located in cytosol; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDCA7L	NM_018719.5	c.*271T>G		3_prime_UTR_variant	10/10	ENST00000406877.8	NP_061189.2
CDCA7L	NM_001127370.3	c.*271T>G		3_prime_UTR_variant	11/11		NP_001120842.1
CDCA7L	NM_001127371.3	c.*271T>G		3_prime_UTR_variant	9/9		NP_001120843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDCA7L	ENST00000406877.8	c.*271T>G		3_prime_UTR_variant	10/10	1	NM_018719.5	ENSP00000383986	P1
CDCA7L	ENST00000356195.9	c.*271T>G		3_prime_UTR_variant	11/11	2		ENSP00000348523
CDCA7L	ENST00000373934.4	c.*271T>G		3_prime_UTR_variant	9/9	2		ENSP00000363045
CDCA7L	ENST00000488845.1	n.793T>G		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51181 AN: 151998 Hom.: 8861 Cov.: 34

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.343 AC: 108606 AN: 316702 Hom.: 19653 Cov.: 3 AF XY: 0.339 AC XY: 56317 AN XY: 166012

Gnomad4 AFR exome AF: 0.281

Gnomad4 AMR exome AF: 0.320

Gnomad4 ASJ exome AF: 0.457

Gnomad4 EAS exome AF: 0.177

Gnomad4 SAS exome AF: 0.266

Gnomad4 FIN exome AF: 0.378

Gnomad4 NFE exome AF: 0.369

Gnomad4 OTH exome AF: 0.352

GnomAD4 genome AF: 0.336 AC: 51175 AN: 152116 Hom.: 8858 Cov.: 34 AF XY: 0.333 AC XY: 24782 AN XY: 74332

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.336

Alfa AF: 0.365 Hom.: 10713

Bravo AF: 0.328

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.0
DANN	Benign	0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs1128226; hg19: chr7-21941669; COSMIC: COSV60991159; COSMIC: COSV60991159;