16-31438677-T-G

Variant names:

• chr16-31438677-T-G
• rs8045738
• NM_001136509.3:c.-335-1493A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136509.3. 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
	ZNF843	NM_001136509.3	MANE Select	c.-335-1493A>C		intron	N/A	NP_001129981.1	Q8N446
	ZNF843	NM_001353381.1		c.-335-1493A>C		intron	N/A	NP_001340310.1	Q8N446

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF843	ENST00000315678.10	TSL:2 MANE Select	c.-335-1493A>C		intron	N/A	ENSP00000322899.5	Q8N446
	ZNF843	ENST00000618063.1	TSL:1	c.-335-1493A>C		intron	N/A	ENSP00000483573.1	Q8N446
	ZNF843	ENST00000857608.1		c.-335-1493A>C		intron	N/A	ENSP00000527667.1

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

African (AFR) AF: 0.836 AC: 34656 AN: 41442

American (AMR) AF: 0.797 AC: 12173 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2660 AN: 3468

East Asian (EAS) AF: 0.577 AC: 2974 AN: 5154

South Asian (SAS) AF: 0.555 AC: 2658 AN: 4788

European-Finnish (FIN) AF: 0.650 AC: 6850 AN: 10544

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47668 AN: 67938

Other (OTH) AF: 0.742 AC: 1564 AN: 2108

Alfa AF: 0.714 Hom.: 149520

Bravo AF: 0.756

Asia WGS AF: 0.564 AC: 1964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		-1.5
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: rs8045738; hg19: chr16-31449998;