rs6015450

chr20-59176062-A-G

Variant summary

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

The NM_178457.3(ZNF831):c.-37+11855A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,186 control chromosomes in the GnomAD database, including 1,602 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 0.14 (1602 hom., cov: 32)
• Consequence: ZNF831 NM_178457.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF831	NM_178457.3	c.-37+11855A>G		intron_variant		ENST00000371030.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF831	ENST00000371030.4	c.-37+11855A>G		intron_variant		1	NM_178457.3	P1
ZNF831	ENST00000637017.1	c.-36-14922A>G		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21022 AN: 152068 Hom.: 1596 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0604

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.138 AC: 21041 AN: 152186 Hom.: 1602 Cov.: 32 AF XY: 0.137 AC XY: 10217 AN XY: 74408

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.0812

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0600

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.110

Alfa AF: 0.125 Hom.: 1277

Bravo AF: 0.133

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.53
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6015450; hg19: chr20-57751117;