rs8109631

Variant names:

• chr19-53576890-A-C
• rs8109631
• NM_001079906.2:c.330A>C

Your query was ambiguous. Multiple possible variants found:

• chr19-53576890-A-C
• chr19-53576890-A-G
• chr19-53576890-A-T

Variant summary

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

The NM_001079906.2(ZNF331):​c.330A>C​(p.Arg110Ser) 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. 16/22 in silico tools predict 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: 31)
• Consequence: ZNF331 NM_001079906.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 24 publications found

Genes affected

ZNF331 (HGNC:15489): (zinc finger protein 331) This gene encodes a zinc finger protein containing a KRAB (Kruppel-associated box) domain found in transcriptional repressors. This gene may be methylated and silenced in cancer cells. This gene is located within a differentially methylated region (DMR) and shows allele-specific expression in placenta. Alternative splicing and the use of alternative promoters results in multiple transcript variants encoding the same protein. [provided by RefSeq, Nov 2015]

ENSG00000290755 (HGNC:):

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=0.055191815).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001079906.2. 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
	ZNF331	NM_001079906.2	MANE Select	c.330A>C	p.Arg110Ser	missense	Exon 6 of 6	NP_001073375.1	Q9NQX6
	ZNF331	NM_001079907.1		c.330A>C	p.Arg110Ser	missense	Exon 6 of 6	NP_001073376.1	Q9NQX6
	ZNF331	NM_001253798.2		c.330A>C	p.Arg110Ser	missense	Exon 7 of 7	NP_001240727.1	Q9NQX6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF331	ENST00000449416.6	TSL:5 MANE Select	c.330A>C	p.Arg110Ser	missense	Exon 6 of 6	ENSP00000393817.1	Q9NQX6
	ZNF331	ENST00000253144.13	TSL:1	c.330A>C	p.Arg110Ser	missense	Exon 7 of 7	ENSP00000253144.9	Q9NQX6
	ZNF331	ENST00000504493.6	TSL:1	c.330A>C	p.Arg110Ser	missense	Exon 5 of 5	ENSP00000425517.2	Q9NQX6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 58

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	0.16
DANN	Benign	0.84
DEOGEN2	Benign	0.056	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.032	N
LIST_S2	Benign	0.11	T
M_CAP	Benign	0.0012	T
MetaRNN	Benign	0.055	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.3	L
PhyloP100		-0.64
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-0.15	N
REVEL	Benign	0.034
Sift	Benign	0.64	T
Sift4G	Benign	0.31	T
Polyphen		0.0	B
Vest4		0.072
MutPred		0.47		Loss of MoRF binding (P = 0.015)
MVP		0.38
MPC		0.68
ClinPred		0.033	T
GERP RS		-5.3
Varity_R		0.057
gMVP		0.12
Mutation Taster		=99/1	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: rs8109631; hg19: chr19-54080144;