rs10411195

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031218.4. 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
	ZNF93	NM_031218.4	MANE Select	c.227-7815T>C		intron	N/A	NP_112495.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF93	ENST00000343769.6	TSL:1 MANE Select	c.227-7815T>C		intron	N/A	ENSP00000342002.4	P35789-1
	ZNF93	ENST00000592160.5	TSL:1	c.227-6641T>C		intron	N/A	ENSP00000467377.1	K7EPG7
	ZNF93	ENST00000588146.1	TSL:4	c.35-7815T>C		intron	N/A	ENSP00000467553.1	K7EPV7

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

African (AFR) AF: 0.209 AC: 8693 AN: 41516

American (AMR) AF: 0.0334 AC: 511 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3472

East Asian (EAS) AF: 0.0576 AC: 298 AN: 5178

South Asian (SAS) AF: 0.122 AC: 586 AN: 4820

European-Finnish (FIN) AF: 0.0132 AC: 140 AN: 10618

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0217 AC: 1475 AN: 68024

Other (OTH) AF: 0.0582 AC: 123 AN: 2112

Alfa AF: 0.0402 Hom.: 1042

Bravo AF: 0.0822

Asia WGS AF: 0.0890 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.57
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10411195; hg19: chr19-20036176;