rs259964

Variant names:

• chr20-59249254-A-G
• rs259964
• NM_178457.3:c.4028-3724A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-59249254-A-G
• chr20-59249254-A-T

Variant summary

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

The NM_178457.3(ZNF831):​c.4028-3724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,828 control chromosomes in the GnomAD database, including 21,292 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 0.51 (21292 hom., cov: 31)
• Consequence: ZNF831 NM_178457.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 42 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=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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.4028-3724A>G		intron	N/A	NP_848552.1	Q5JPB2
	ZNF831	NM_001384354.1		c.4028-3724A>G		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.4028-3724A>G		intron	N/A	ENSP00000360069.2	Q5JPB2
	ZNF831	ENST00000637017.1	TSL:5	c.4028-3724A>G		intron	N/A	ENSP00000490240.1	Q5JPB2

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77974 AN: 151710 Hom.: 21296 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.514 AC: 77991 AN: 151828 Hom.: 21292 Cov.: 31 AF XY: 0.523 AC XY: 38774 AN XY: 74198

African (AFR) AF: 0.345 AC: 14265 AN: 41322

American (AMR) AF: 0.571 AC: 8722 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1969 AN: 3458

East Asian (EAS) AF: 0.888 AC: 4586 AN: 5162

South Asian (SAS) AF: 0.778 AC: 3746 AN: 4816

European-Finnish (FIN) AF: 0.595 AC: 6279 AN: 10546

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36704 AN: 67940

Other (OTH) AF: 0.536 AC: 1128 AN: 2106

Alfa AF: 0.523 Hom.: 22264

Bravo AF: 0.500

Asia WGS AF: 0.795 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.022
DANN	Benign	0.31
PhyloP100		-1.7
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: rs259964; hg19: chr20-57824309;