NM_178457.3:c.-36-7319A>G

Variant names:

• chr20-59183665-A-G
• rs16982520
• NM_178457.3:c.-36-7319A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178457.3(ZNF831):​c.-36-7319A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,186 control chromosomes in the GnomAD database, including 1,455 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 (1455 hom., cov: 32)
• Consequence: ZNF831 NM_178457.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 25 publications found

Genes affected

ZNF831 (HGNC:16167): (zinc finger protein 831) Predicted to enable metal ion binding activity. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178457.3. 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
	ZNF831	NM_178457.3	MANE Select	c.-36-7319A>G		intron	N/A	NP_848552.1
	ZNF831	NM_001384354.1		c.-36-7319A>G		intron	N/A	NP_001371283.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF831	ENST00000371030.4	TSL:1 MANE Select	c.-36-7319A>G		intron	N/A	ENSP00000360069.2
	ZNF831	ENST00000637017.1	TSL:5	c.-36-7319A>G		intron	N/A	ENSP00000490240.1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20037 AN: 152068 Hom.: 1453 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.132 AC: 20047 AN: 152186 Hom.: 1455 Cov.: 32 AF XY: 0.131 AC XY: 9770 AN XY: 74412

African (AFR) AF: 0.173 AC: 7163 AN: 41506

American (AMR) AF: 0.0787 AC: 1204 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 484 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0593 AC: 286 AN: 4822

European-Finnish (FIN) AF: 0.164 AC: 1740 AN: 10580

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8744 AN: 68002

Other (OTH) AF: 0.105 AC: 223 AN: 2116

Alfa AF: 0.124 Hom.: 2062

Bravo AF: 0.126

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.27
PhyloP100		-0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs16982520; hg19: chr20-57758720;