10-38112489-C-G

Position:

• chr10-38112489-C-G

Variant summary

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

The NM_001324250.3(ZNF37A):​c.16-2266C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,540 control chromosomes in the GnomAD database, including 13,032 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 0.41 (13032 hom., cov: 29)
• Consequence: ZNF37A NM_001324250.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

Genes affected

ZNF37A (HGNC:13102): (zinc finger protein 37A) 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 by RNA polymerase II. 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 (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF37A	NM_001324250.3	c.16-2266C>G		intron_variant		ENST00000685332.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF37A	ENST00000685332.1	c.16-2266C>G		intron_variant			NM_001324250.3	P1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62300 AN: 151436 Hom.: 12998 Cov.: 29

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.412 AC: 62388 AN: 151540 Hom.: 13032 Cov.: 29 AF XY: 0.407 AC XY: 30132 AN XY: 74020

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.426

Alfa AF: 0.267 Hom.: 642

Bravo AF: 0.430

Asia WGS AF: 0.405 AC: 1411 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	3.2
DANN	Benign	0.58

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: rs176880; hg19: chr10-38401417;