chr20-59215381-A-C

Variant names:

• chr20-59215381-A-C
• rs12625057
• NM_178457.3:c.4027+8325A>C

Variant summary

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

The NM_178457.3(ZNF831):​c.4027+8325A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 152,308 control chromosomes in the GnomAD database, including 670 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 0.069 (670 hom., cov: 33)
• Consequence: ZNF831 NM_178457.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 9 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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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.4027+8325A>C		intron	N/A	NP_848552.1	Q5JPB2
	ZNF831	NM_001384354.1		c.4027+8325A>C		intron	N/A	NP_001371283.1	Q5JPB2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF831	ENST00000371030.4	TSL:1 MANE Select	c.4027+8325A>C		intron	N/A	ENSP00000360069.2	Q5JPB2
	ZNF831	ENST00000637017.1	TSL:5	c.4027+8325A>C		intron	N/A	ENSP00000490240.1	Q5JPB2

Frequencies

GnomAD3 genomes AF: 0.0692 AC: 10530 AN: 152190 Hom.: 670 Cov.: 33

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0613

Gnomad OTH AF: 0.0857

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

GnomAD4 genome AF: 0.0692 AC: 10535 AN: 152308 Hom.: 670 Cov.: 33 AF XY: 0.0730 AC XY: 5439 AN XY: 74476

African (AFR) AF: 0.0179 AC: 745 AN: 41568

American (AMR) AF: 0.155 AC: 2372 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0596 AC: 207 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1478 AN: 5182

South Asian (SAS) AF: 0.115 AC: 555 AN: 4824

European-Finnish (FIN) AF: 0.0719 AC: 763 AN: 10618

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

European-Non Finnish (NFE) AF: 0.0613 AC: 4173 AN: 68026

Other (OTH) AF: 0.0848 AC: 179 AN: 2110

Alfa AF: 0.0719 Hom.: 1264

Bravo AF: 0.0745

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.81
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs12625057; hg19: chr20-57790436;