rs2127407

Positions:

• chr19-21370388-G-A

Variant summary

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

The NM_001355237.2(ZNF738):​c.97-4850G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,944 control chromosomes in the GnomAD database, including 24,591 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 0.57 (24591 hom., cov: 32)
• Consequence: ZNF738 NM_001355237.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

ZNF738 (HGNC:32469): (zinc finger protein 738) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein polyubiquitination. 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=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF738	NM_001355237.2	c.97-4850G>A		intron_variant		ENST00000683779.1	NP_001342166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF738	ENST00000683779.1	c.97-4850G>A		intron_variant			NM_001355237.2	ENSP00000507366	P1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85913 AN: 151828 Hom.: 24580 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.566 AC: 85953 AN: 151944 Hom.: 24591 Cov.: 32 AF XY: 0.564 AC XY: 41903 AN XY: 74284

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.591

Alfa AF: 0.554 Hom.: 2907

Bravo AF: 0.572

Asia WGS AF: 0.580 AC: 2010 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.91

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: rs2127407; hg19: chr19-21553190;