dbSNP rs11436: ZCCHC17:c.*280T>C (chr1-31364473-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016505.4(ZCCHC17):c.*280T>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 0.553 in 453,152 control chromosomes in the GnomAD database, including 73,108 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 0.54 ( 23364 hom., cov: 31)

Exomes 𝑓: 0.56 ( 49744 hom. )

Consequence

ZCCHC17
NM_016505.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.911

Variant links:

Genes affected

ZCCHC17 (HGNC:30246): (zinc finger CCHC-type containing 17) Enables identical protein binding activity. Predicted to be involved in RNA stabilization. Predicted to be located in nucleolus. Predicted to be part of cytosolic large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]

ZCCHC17 links:

FABP3 (HGNC:3557): (fatty acid binding protein 3) The intracellular fatty acid-binding proteins (FABPs) belongs to a multigene family. FABPs are divided into at least three distinct types, namely the hepatic-, intestinal- and cardiac-type. They form 14-15 kDa proteins and are thought to participate in the uptake, intracellular metabolism and/or transport of long-chain fatty acids. They may also be responsible in the modulation of cell growth and proliferation. Fatty acid-binding protein 3 gene contains four exons and its function is to arrest growth of mammary epithelial cells. This gene is a candidate tumor suppressor gene for human breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

FABP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZCCHC17	NM_016505.4 link	c.*280T>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000344147.10	NP_057589.2	Q9NP64-1B4DYA9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZCCHC17	ENST00000344147.10 link	c.*280T>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_016505.4	ENSP00000343557.5		Q9NP64-1

Frequencies

GnomAD3 genomes

AF:

0.544

AC:

82650

AN:

151906

Hom.:

23365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.512

Gnomad AMR

AF:

0.554

Gnomad ASJ

AF:

0.641

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.623

Gnomad OTH

AF:

0.558

GnomAD4 exome

AF:

0.557

AC:

167823

AN:

301128

Hom.:

49744

Cov.:

AF XY:

0.552

AC XY:

85121

AN XY:

154342

show subpopulations

Gnomad4 AFR exome

AF:

0.461

Gnomad4 AMR exome

AF:

0.529

Gnomad4 ASJ exome

AF:

0.653

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.357

Gnomad4 FIN exome

AF:

0.574

Gnomad4 NFE exome

AF:

0.625

Gnomad4 OTH exome

AF:

0.566

GnomAD4 genome

AF:

0.544

AC:

82656

AN:

152024

Hom.:

23364

Cov.:

AF XY:

0.535

AC XY:

39778

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.461

Gnomad4 AMR

AF:

0.554

Gnomad4 ASJ

AF:

0.641

Gnomad4 EAS

AF:

0.191

Gnomad4 SAS

AF:

0.351

Gnomad4 FIN

AF:

0.573

Gnomad4 NFE

AF:

0.623

Gnomad4 OTH

AF:

0.554

Alfa

AF:

0.609

Hom.:

12056

Bravo

AF:

0.540

Asia WGS

AF:

0.283

AC:

987

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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