7-149776375-G-T

Variant names:

• chr7-149776375-G-T
• rs371687744
• ENST00000882861.1:c.-182C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000882861.1(ZNF467):​c.-182C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000825 in 1,211,392 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
  • Exomes 𝑓: 8.3e-7 (0 hom.)
• Consequence: ZNF467 ENST00000882861.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 0 publications found

Genes affected

ZNF467 (HGNC:23154): (zinc finger protein 467) The protein encoded by this gene is a zinc finger protein whose function has not yet been elucidated in humans. However, the mouse ortholog of this protein enhances adipocyte differentiation and suppresses osteoblast differentiation in bone marrow. The mouse protein also is a transcription factor for several genes and can help recruit histone deacetylase complexes. [provided by RefSeq, Aug 2016]

SSPOP (HGNC:21998): (SCO-spondin, pseudogene) Predicted to enable peptidase inhibitor activity. Predicted to be involved in several processes, including cell adhesion; negative regulation of catalytic activity; and regulation of peptidase activity. Predicted to be located in cytoplasm. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000293556 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.039096802).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000882861.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSPOP	NR_163594.1		n.80G>T		non_coding_transcript_exon	Exon 2 of 103

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF467	ENST00000882861.1		c.-182C>A		5_prime_UTR	Exon 1 of 5	ENSP00000552920.1
	ZNF467	ENST00000882862.1		c.-446C>A		5_prime_UTR	Exon 1 of 7	ENSP00000552921.1
	ZNF467	ENST00000882863.1		c.-558C>A		5_prime_UTR	Exon 1 of 7	ENSP00000552922.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 8.25e-7 AC: 1 AN: 1211392 Hom.: 0 Cov.: 31 AF XY: 0.00000167 AC XY: 1 AN XY: 599922

African (AFR) AF: 0.00 AC: 0 AN: 26262

American (AMR) AF: 0.00 AC: 0 AN: 36956

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16792

East Asian (EAS) AF: 0.00 AC: 0 AN: 16714

South Asian (SAS) AF: 0.00 AC: 0 AN: 82396

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31300

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4426

European-Non Finnish (NFE) AF: 0.00000105 AC: 1 AN: 952698

Other (OTH) AF: 0.00 AC: 0 AN: 43848

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	2.8
DANN	Benign	0.59
DEOGEN2	Benign	0.012	T
FATHMM_MKL	Benign	0.083	N
LIST_S2	Benign	0.52	T
MetaRNN	Benign	0.039	T
MutationAssessor	Benign	0.34	N
PhyloP100		0.025
PrimateAI	Benign	0.21	T
Sift4G	Benign	0.20	T
Polyphen		0.0	B
Vest4		0.14
MVP		0.16
GERP RS		-0.76
Varity_R		0.094
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs371687744; hg19: chr7-149473464;