rs78797427

Variant names:

• chr19-57720878-C-G
• rs78797427
• NM_024833.3:c.1208G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-57720878-C-G
• chr19-57720878-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_024833.3(ZNF671):​c.1208G>C​(p.Gly403Ala) variant causes a missense 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G403E) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZNF671 NM_024833.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769

Genes affected

ZNF671 (HGNC:26279): (zinc finger protein 671) Predicted to enable DNA-binding transcription factor activity 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 located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000269026 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.38081664).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF671	NM_024833.3	c.1208G>C	p.Gly403Ala	missense_variant	Exon 4 of 4	ENST00000317398.10	NP_079109.2
ZNF671	NM_001321376.2	c.977G>C	p.Gly326Ala	missense_variant	Exon 5 of 5		NP_001308305.1
ZNF671	NM_001321375.2	c.914G>C	p.Gly305Ala	missense_variant	Exon 3 of 3		NP_001308304.1
ZNF671	XM_017027314.2	c.977G>C	p.Gly326Ala	missense_variant	Exon 4 of 4		XP_016882803.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF671	ENST00000317398.10	c.1208G>C	p.Gly403Ala	missense_variant	Exon 4 of 4	1	NM_024833.3	ENSP00000321848.5
ENSG00000269026	ENST00000594684.1	c.34-29907C>G		intron_variant	Intron 1 of 2	1		ENSP00000472160.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.63
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	20
DANN	Uncertain	1.0
DEOGEN2	Benign	0.25	T
Eigen	Benign	-0.090
Eigen_PC	Benign	-0.37
FATHMM_MKL	Benign	0.42	N
LIST_S2	Benign	0.77	T
M_CAP	Benign	0.0051	T
MetaRNN	Benign	0.38	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.1	M
PrimateAI	Benign	0.45	T
PROVEAN	Pathogenic	-5.7	D
REVEL	Benign	0.036
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0050	D
Polyphen		1.0	D
Vest4		0.20
MutPred		0.69		Loss of ubiquitination at K404 (P = 0.0896);
MVP		0.55
MPC		0.68
ClinPred		0.97	D
GERP RS		0.81
Varity_R		0.47
gMVP		0.082

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: rs78797427; hg19: chr19-58232246;