Variant 19-41323676-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_052848.3(CCDC97):c.*961T>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 0.146 in 155,252 control chromosomes in the GnomAD database, including 1,916 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 ( 1886 hom., cov: 32)

Exomes 𝑓: 0.12 ( 30 hom. )

Consequence

CCDC97
NM_052848.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0790

Variant links:

Genes affected

CCDC97 (HGNC:28289): (coiled-coil domain containing 97)

CCDC97 links:

TGFB1 (HGNC:11766): (transforming growth factor beta 1) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate a latency-associated peptide (LAP) and a mature peptide, and is found in either a latent form composed of a mature peptide homodimer, a LAP homodimer, and a latent TGF-beta binding protein, or in an active form consisting solely of the mature peptide homodimer. The mature peptide may also form heterodimers with other TGFB family members. This encoded protein regulates cell proliferation, differentiation and growth, and can modulate expression and activation of other growth factors including interferon gamma and tumor necrosis factor alpha. This gene is frequently upregulated in tumor cells, and mutations in this gene result in Camurati-Engelmann disease. [provided by RefSeq, Aug 2016]

TGFB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC97	NM_052848.3 linkuse as main transcript	c.*961T>A		3_prime_UTR_variant	5/5	ENST00000269967.4
CCDC97	NM_001346100.2 linkuse as main transcript	c.*961T>A		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC97	ENST00000269967.4 linkuse as main transcript	c.*961T>A		3_prime_UTR_variant	5/5	1	NM_052848.3	P1
TGFB1	ENST00000598758.5 linkuse as main transcript	n.302+8452A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22338

AN:

151860

Hom.:

1890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0850

Gnomad AMI

AF:

0.407

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.0999

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.121

AC:

397

AN:

3274

Hom.:

Cov.:

AF XY:

0.117

AC XY:

217

AN XY:

1856

show subpopulations

Gnomad4 AFR exome

AF:

0.0577

Gnomad4 AMR exome

AF:

0.0769

Gnomad4 ASJ exome

AF:

0.0606

Gnomad4 EAS exome

AF:

0.124

Gnomad4 SAS exome

AF:

0.0862

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.118

Gnomad4 OTH exome

AF:

0.154

GnomAD4 genome

AF:

0.147

AC:

22330

AN:

151978

Hom.:

1886

Cov.:

AF XY:

0.144

AC XY:

10724

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.0849

Gnomad4 AMR

AF:

0.141

Gnomad4 ASJ

AF:

0.196

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.150

Gnomad4 NFE

AF:

0.173

Gnomad4 OTH

AF:

0.170

Alfa

AF:

0.152

Hom.:

241

Bravo

AF:

0.148

Asia WGS

AF:

0.193

AC:

673

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.91

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over