16-3232605-T-C

Variant names:

• chr16-3232605-T-C
• rs2075852
• NM_198088.3:c.340-58A>G

Variant summary

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

The NM_198088.3(ZNF200):​c.340-58A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,596,994 control chromosomes in the GnomAD database, including 183,865 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 0.44 (14939 hom., cov: 32)
  • Exomes 𝑓: 0.48 (168926 hom.)
• Consequence: ZNF200 NM_198088.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 16 publications found

Genes affected

ZNF200 (HGNC:12993): (zinc finger protein 200) Predicted to enable metal ion binding activity. Predicted to be located in nucleus. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF200	NM_198088.3	c.340-58A>G		intron_variant	Intron 3 of 4	ENST00000414144.7	NP_932354.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF200	ENST00000414144.7	c.340-58A>G		intron_variant	Intron 3 of 4	1	NM_198088.3	ENSP00000405786.2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66080 AN: 151816 Hom.: 14923 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.480 AC: 694247 AN: 1445060 Hom.: 168926 Cov.: 33 AF XY: 0.478 AC XY: 343313 AN XY: 718812

African (AFR) AF: 0.292 AC: 9559 AN: 32784

American (AMR) AF: 0.645 AC: 27701 AN: 42946

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 11101 AN: 25192

East Asian (EAS) AF: 0.582 AC: 23057 AN: 39636

South Asian (SAS) AF: 0.422 AC: 35491 AN: 84062

European-Finnish (FIN) AF: 0.489 AC: 23705 AN: 48452

Middle Eastern (MID) AF: 0.430 AC: 2437 AN: 5672

European-Non Finnish (NFE) AF: 0.482 AC: 533223 AN: 1106532

Other (OTH) AF: 0.468 AC: 27973 AN: 59784

GnomAD4 genome AF: 0.435 AC: 66130 AN: 151934 Hom.: 14939 Cov.: 32 AF XY: 0.438 AC XY: 32538 AN XY: 74254

African (AFR) AF: 0.303 AC: 12540 AN: 41444

American (AMR) AF: 0.534 AC: 8151 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3466

East Asian (EAS) AF: 0.582 AC: 2994 AN: 5144

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4816

European-Finnish (FIN) AF: 0.483 AC: 5080 AN: 10526

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32398 AN: 67958

Other (OTH) AF: 0.435 AC: 916 AN: 2108

Alfa AF: 0.462 Hom.: 21479

Bravo AF: 0.440

Asia WGS AF: 0.482 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.49
PhyloP100		0.0040
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: rs2075852; hg19: chr16-3282605; COSMIC: COSV107504259; COSMIC: COSV107504259;