chr11-3377432-G-A

Position:

• chr11-3377432-G-A

Variant summary

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

The NM_001130520.3(ZNF195):​c.3+1606C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,162 control chromosomes in the GnomAD database, including 1,741 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 0.13 (1741 hom., cov: 33)
• Consequence: ZNF195 NM_001130520.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349

Genes affected

ZNF195 (HGNC:12986): (zinc finger protein 195) This gene encodes a protein belonging to the Krueppel C2H2-type zinc-finger protein family. These family members are transcription factors that are implicated in a variety of cellular processes. This gene is located near the centromeric border of chromosome 11p15.5, next to an imprinted domain that is associated with maternal-specific loss of heterozygosity in Wilms' tumors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF195	NM_001130520.3	c.3+1606C>T		intron_variant		ENST00000399602.9	NP_001123992.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF195	ENST00000399602.9	c.3+1606C>T		intron_variant		1	NM_001130520.3	ENSP00000382511	A2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20506 AN: 152044 Hom.: 1747 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.135 AC: 20491 AN: 152162 Hom.: 1741 Cov.: 33 AF XY: 0.138 AC XY: 10271 AN XY: 74392

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.125

Alfa AF: 0.121 Hom.: 1150

Bravo AF: 0.132

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
DANN	Benign	0.26

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: rs10833833; hg19: chr11-3398662;