rs10411195

Variant names:

• chr19-19925367-T-C
• rs10411195
• NM_031218.4:c.227-7815T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031218.4(ZNF93):​c.227-7815T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,248 control chromosomes in the GnomAD database, including 977 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 0.078 (977 hom., cov: 31)
• Consequence: ZNF93 NM_031218.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

ZNF93 (HGNC:13169): (zinc finger protein 93) Enables DNA-binding transcription factor activity. Involved in negative regulation of transcription, DNA-templated and negative regulation of transposon integration. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF93	NM_031218.4	c.227-7815T>C		intron_variant	Intron 3 of 3	ENST00000343769.6	NP_112495.2
ZNF93	XM_047439495.1	c.131-7815T>C		intron_variant	Intron 3 of 3		XP_047295451.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF93	ENST00000343769.6	c.227-7815T>C		intron_variant	Intron 3 of 3	1	NM_031218.4	ENSP00000342002.4

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11849 AN: 152130 Hom.: 974 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0334

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0780 AC: 11873 AN: 152248 Hom.: 977 Cov.: 31 AF XY: 0.0778 AC XY: 5793 AN XY: 74444

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.0576

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0217

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0331 Hom.: 299

Bravo AF: 0.0822

Asia WGS AF: 0.0890 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.57

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

Other links and lift over

dbSNP: rs10411195; hg19: chr19-20036176;