NM_175884.6:c.*1231T>C

Variant names:

• chr7-106658958-A-G
• rs2190093
• NM_175884.6:c.*1231T>C

Variant summary

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

The NM_175884.6(CCDC71L):​c.*1231T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,188 control chromosomes in the GnomAD database, including 2,375 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 0.15 (2375 hom., cov: 32)
  • Exomes 𝑓: 0.11 (0 hom.)
• Consequence: CCDC71L NM_175884.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

Genes affected

CCDC71L (HGNC:26685): (coiled-coil domain containing 71 like) Predicted to be involved in cellular lipid metabolic process and positive regulation of fat cell differentiation. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000243797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC71L	NM_175884.6	c.*1231T>C		3_prime_UTR_variant	Exon 1 of 1	ENST00000523505.3	NP_787080.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC71L	ENST00000523505	c.*1231T>C		3_prime_UTR_variant	Exon 1 of 1		NM_175884.6	ENSP00000430897.2
ENSG00000243797	ENST00000490856.5	n.109-48495T>C		intron_variant	Intron 1 of 4	4
ENSG00000243797	ENST00000592441.1	n.173-48495T>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22924 AN: 152040 Hom.: 2379 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.107 AC: 3 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

Gnomad4 FIN exome AF: 0.115

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.151 AC: 22921 AN: 152160 Hom.: 2375 Cov.: 32 AF XY: 0.154 AC XY: 11451 AN XY: 74358

Gnomad4 AFR AF: 0.0565

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.127

Alfa AF: 0.154 Hom.: 2033

Bravo AF: 0.145

Asia WGS AF: 0.406 AC: 1410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.5
DANN	Benign	0.71

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: rs2190093; hg19: chr7-106299404;