chr16-3317061-G-A

Position:

• chr16-3317061-G-A

Variant summary

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

The NM_001302109.2(ZNF75A):​c.934+39G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,575,034 control chromosomes in the GnomAD database, including 39,200 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 0.21 (3724 hom., cov: 32)
  • Exomes 𝑓: 0.22 (35476 hom.)
• Consequence: ZNF75A NM_001302109.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

ZNF75A (HGNC:13146): (zinc finger protein 75A) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF75A	NM_001302109.2	c.934+39G>A		intron_variant		ENST00000669516.2	NP_001289038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF75A	ENST00000669516.2	c.934+39G>A		intron_variant			NM_001302109.2	ENSP00000499415	P1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32563 AN: 151930 Hom.: 3723 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.202

GnomAD3 exomes AF: 0.221 AC: 51624 AN: 233216 Hom.: 6387 AF XY: 0.213 AC XY: 26820 AN XY: 125888

Gnomad AFR exome AF: 0.183

Gnomad AMR exome AF: 0.346

Gnomad ASJ exome AF: 0.208

Gnomad EAS exome AF: 0.0426

Gnomad SAS exome AF: 0.108

Gnomad FIN exome AF: 0.289

Gnomad NFE exome AF: 0.236

Gnomad OTH exome AF: 0.224

GnomAD4 exome AF: 0.217 AC: 308729 AN: 1422986 Hom.: 35476 Cov.: 25 AF XY: 0.213 AC XY: 150887 AN XY: 708650

Gnomad4 AFR exome AF: 0.179

Gnomad4 AMR exome AF: 0.328

Gnomad4 ASJ exome AF: 0.198

Gnomad4 EAS exome AF: 0.0380

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.281

Gnomad4 NFE exome AF: 0.228

Gnomad4 OTH exome AF: 0.198

GnomAD4 genome AF: 0.214 AC: 32578 AN: 152048 Hom.: 3724 Cov.: 32 AF XY: 0.215 AC XY: 16015 AN XY: 74330

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0373

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.199

Alfa AF: 0.226 Hom.: 1039

Bravo AF: 0.216

Asia WGS AF: 0.0810 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.60

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: rs17611827; hg19: chr16-3367061; COSMIC: COSV73039566; COSMIC: COSV73039566;