rs6070744

chr20-59215563-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178457.3(ZNF831):c.4027+8507T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 152,298 control chromosomes in the GnomAD database, including 787 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 0.090 (787 hom., cov: 33)
• Consequence: ZNF831 NM_178457.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF831	NM_178457.3	c.4027+8507T>C		intron_variant		ENST00000371030.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF831	ENST00000371030.4	c.4027+8507T>C		intron_variant		1	NM_178457.3	P1
ZNF831	ENST00000637017.1	c.4027+8507T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13730 AN: 152180 Hom.: 789 Cov.: 33

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0901 AC: 13725 AN: 152298 Hom.: 787 Cov.: 33 AF XY: 0.0885 AC XY: 6588 AN XY: 74464

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.0900

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.0993

Alfa AF: 0.118 Hom.: 714

Bravo AF: 0.0859

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.010
Dann	Benign	0.65

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: rs6070744; hg19: chr20-57790618;