dbSNP rs3740329: LOC105378268:n.334C>A (chr10-42638638-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007062124.1(LOC105378268):n.334C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 401,038 control chromosomes in the GnomAD database, including 10,137 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 0.23 ( 4928 hom., cov: 36)

Exomes 𝑓: 0.19 ( 5209 hom. )

Consequence

LOC105378268
XR_007062124.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29

Variant links:

Genes affected

LOC105378268 (HGNC:):

LOC105378268 links:

ZNF33B (HGNC:13097): (zinc finger protein 33B) This gene encodes a member of the zinc finger family of proteins. This gene shows decreased expression in cumulus cells derived from patients undergoing controlled ovarian stimulation. This gene is present in a gene cluster with several related zinc finger genes in the pericentromeric region of chromosome 10. Pseudogenes have been identified on chromosomes 7 and 10. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

ZNF33B 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=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF33B	NM_006955.3 link	c.-209G>T		upstream_gene_variant		ENST00000359467.8	NP_008886.1	Q06732

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF33B	ENST00000359467.8 link	c.-209G>T		upstream_gene_variant		1	NM_006955.3	ENSP00000352444.2		Q06732

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35288

AN:

152182

Hom.:

4908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.306

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.216

GnomAD4 exome

AF:

0.191

AC:

47630

AN:

248738

Hom.:

5209

AF XY:

0.198

AC XY:

28457

AN XY:

143516

show subpopulations

Gnomad4 AFR exome

AF:

0.405

Gnomad4 AMR exome

AF:

0.176

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.128

Gnomad4 SAS exome

AF:

0.289

Gnomad4 FIN exome

AF:

0.253

Gnomad4 NFE exome

AF:

0.147

Gnomad4 OTH exome

AF:

0.193

GnomAD4 genome

AF:

0.232

AC:

35349

AN:

152300

Hom.:

4928

Cov.:

AF XY:

0.238

AC XY:

17716

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.176

Gnomad4 ASJ

AF:

0.216

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.304

Gnomad4 FIN

AF:

0.280

Gnomad4 NFE

AF:

0.148

Gnomad4 OTH

AF:

0.218

Alfa

AF:

0.195

Hom.:

546

Bravo

AF:

0.227

Asia WGS

AF:

0.223

AC:

777

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.1

DANN

Benign

0.62

Splicing

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