7-106658958-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_175884.6(CCDC71L):​c.*1231T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

CCDC71L
NM_175884.6 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.180
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC71LNM_175884.6 linkc.*1231T>A 3_prime_UTR_variant Exon 1 of 1 ENST00000523505.3 NP_787080.2 Q8N9Z2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC71LENST00000523505 linkc.*1231T>A 3_prime_UTR_variant Exon 1 of 1 NM_175884.6 ENSP00000430897.2 Q8N9Z2-1
ENSG00000243797ENST00000490856.5 linkn.109-48495T>A intron_variant Intron 1 of 4 4
ENSG00000243797ENST00000592441.1 linkn.173-48495T>A intron_variant Intron 2 of 4 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
4.2
DANN
Benign
0.68

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2190093; hg19: chr7-106299404; API