chr19-52572344-C-A

Variant names:

• chr19-52572344-C-A
• rs970161098
• ENST00000301093.6:c.103C>A

Variant summary

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

The NM_018260.3(ZNF701):​c.-71-1733C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 0.0000088 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF701 NM_018260.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 0 publications found

Genes affected

ZNF701 (HGNC:25597): (zinc finger protein 701) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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=0.04344386).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF701	NM_018260.3	c.-71-1733C>A		intron_variant	Intron 1 of 3	ENST00000391785.8	NP_060730.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF701	ENST00000391785.8	c.-71-1733C>A		intron_variant	Intron 1 of 3	1	NM_018260.3	ENSP00000375662.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00000782 AC: 1 AN: 127876 AF XY: 0.0000143

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000211

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000881 AC: 10 AN: 1135022 Hom.: 0 Cov.: 29 AF XY: 0.00000718 AC XY: 4 AN XY: 556900

African (AFR) AF: 0.00 AC: 0 AN: 24362

American (AMR) AF: 0.00 AC: 0 AN: 28164

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15902

East Asian (EAS) AF: 0.00 AC: 0 AN: 12808

South Asian (SAS) AF: 0.00 AC: 0 AN: 76116

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12640

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4388

European-Non Finnish (NFE) AF: 0.00000870 AC: 8 AN: 919200

Other (OTH) AF: 0.0000483 AC: 2 AN: 41442

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.40	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.63
DANN	Benign	0.92
DEOGEN2	Benign	0.0020	T;.;T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.0026	N
LIST_S2	Benign	0.040	.;T;T
M_CAP	Benign	0.0026	T
MetaRNN	Benign	0.043	T;T;T
MetaSVM	Benign	-0.88	T
PhyloP100		-1.0
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.34	N;.;N
REVEL	Benign	0.028
Sift	Pathogenic	0.0	D;.;D
Sift4G	Benign	0.26	T;T;T
Vest4		0.11
MutPred		0.23		Gain of glycosylation at R35 (P = 0.0306);Gain of glycosylation at R35 (P = 0.0306);Gain of glycosylation at R35 (P = 0.0306);
MVP		0.10
MPC		0.12
ClinPred		0.070	T
GERP RS		-0.28
Varity_R		0.18
gMVP		0.039
Mutation Taster		=100/0	polymorphism

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: rs970161098; hg19: chr19-53075597;