rs2505179

Positions:

• chr10-38126203-G-A

Variant summary

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

The NM_001324256.2(ZNF37A):​c.238+10913G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,038 control chromosomes in the GnomAD database, including 17,910 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 0.48 (17910 hom., cov: 32)
• Consequence: ZNF37A NM_001324256.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF37A	NM_001324256.2	c.238+10913G>A		intron_variant			NP_001311185.1
ZNF37A	NM_001324257.2	c.238+10913G>A		intron_variant			NP_001311186.1
ZNF37A	NM_001324258.2	c.238+10913G>A		intron_variant			NP_001311187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF37A	ENST00000638053.1	c.238+10913G>A		intron_variant		5		ENSP00000490669

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73359 AN: 151920 Hom.: 17876 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.483 AC: 73445 AN: 152038 Hom.: 17910 Cov.: 32 AF XY: 0.477 AC XY: 35423 AN XY: 74324

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.506

Alfa AF: 0.487 Hom.: 3081

Bravo AF: 0.504

Asia WGS AF: 0.476 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505179; hg19: chr10-38415131;