16-31438677-T-G

Position:

• chr16-31438677-T-G

Variant summary

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

The NM_001136509.3(ZNF843):​c.-335-1493A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,910 control chromosomes in the GnomAD database, including 41,773 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 0.74 (41773 hom., cov: 30)
• Consequence: ZNF843 NM_001136509.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

ZNF843 (HGNC:28710): (zinc finger protein 843) 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF843	NM_001136509.3	c.-335-1493A>C		intron_variant		ENST00000315678.10	NP_001129981.1
ZNF843	NM_001353381.1	c.-335-1493A>C		intron_variant			NP_001340310.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF843	ENST00000315678.10	c.-335-1493A>C		intron_variant		2	NM_001136509.3	ENSP00000322899.5
ZNF843	ENST00000618063.1	c.-335-1493A>C		intron_variant		1		ENSP00000483573.1
ZNF843	ENST00000564218.5	c.-335-1493A>C		intron_variant		5		ENSP00000455858.1

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111793 AN: 151790 Hom.: 41700 Cov.: 30

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.737 AC: 111939 AN: 151910 Hom.: 41773 Cov.: 30 AF XY: 0.733 AC XY: 54374 AN XY: 74216

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.742

Alfa AF: 0.709 Hom.: 72121

Bravo AF: 0.756

Asia WGS AF: 0.564 AC: 1964 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	2.2
DANN	Benign	0.41

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: rs8045738; hg19: chr16-31449998;