10-38112489-C-G

Variant names:

• chr10-38112489-C-G
• rs176880
• NM_001324250.3:c.16-2266C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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]

PLD5P1 (HGNC:55072): (PLD5 pseudogene 1) Predicted to be involved in regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000302873 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001324250.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF37A	NM_001324250.3	MANE Select	c.16-2266C>G		intron	N/A	NP_001311179.1	P17032
	ZNF37A	NM_001007094.4		c.16-2266C>G		intron	N/A	NP_001007095.1	P17032
	ZNF37A	NM_001178101.3		c.16-2266C>G		intron	N/A	NP_001171572.1	P17032

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF37A	ENST00000685332.1	MANE Select	c.16-2266C>G		intron	N/A	ENSP00000508865.1	P17032
	ZNF37A	ENST00000351773.7	TSL:1	c.16-2266C>G		intron	N/A	ENSP00000329141.3	P17032
	PLD5P1	ENST00000640275.1	TSL:5	n.16-2266C>G		intron	N/A	ENSP00000491560.1	A0A1W2PQ67

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

African (AFR) AF: 0.415 AC: 17135 AN: 41312

American (AMR) AF: 0.468 AC: 7120 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3464

East Asian (EAS) AF: 0.498 AC: 2564 AN: 5144

South Asian (SAS) AF: 0.248 AC: 1190 AN: 4798

European-Finnish (FIN) AF: 0.316 AC: 3298 AN: 10422

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28370 AN: 67880

Other (OTH) AF: 0.426 AC: 892 AN: 2096

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.58
PhyloP100		-0.28
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: rs176880; hg19: chr10-38401417;