rs4718067

Positions:

• chr7-64356018-G-A
• chr7-64356018-G-C

Variant summary

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

The NM_001170905.3(ZNF736):​c.*6871G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 179,716 control chromosomes in the GnomAD database, including 7,898 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 0.31 (7369 hom., cov: 32)
  • Exomes 𝑓: 0.20 (529 hom.)
• Consequence: ZNF736 NM_001170905.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

ZNF736 (HGNC:32467): (zinc finger protein 736) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TRIM60P18 (HGNC:38490): (tripartite motif containing 60 pseudogene 18)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF736	NM_001170905.3	c.*6871G>A		3_prime_UTR_variant	4/4	ENST00000423484.3	NP_001164376.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF736	ENST00000423484.3	c.*6871G>A		3_prime_UTR_variant	4/4	2	NM_001170905.3	ENSP00000400852	P1
TRIM60P18	ENST00000441518.1	n.647G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46757 AN: 151902 Hom.: 7364 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.298

GnomAD4 exome AF: 0.203 AC: 5628 AN: 27696 Hom.: 529 Cov.: 0 AF XY: 0.199 AC XY: 3283 AN XY: 16488

Gnomad4 AFR exome AF: 0.217

Gnomad4 AMR exome AF: 0.229

Gnomad4 ASJ exome AF: 0.256

Gnomad4 EAS exome AF: 0.163

Gnomad4 SAS exome AF: 0.150

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.308 AC: 46778 AN: 152020 Hom.: 7369 Cov.: 32 AF XY: 0.306 AC XY: 22765 AN XY: 74286

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.297

Alfa AF: 0.309 Hom.: 1131

Bravo AF: 0.310

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4718067; hg19: chr7-63816396;