10-38095711-T-G

Position:

• chr10-38095711-T-G

Variant summary

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

The NM_001324250.3(ZNF37A):​c.-105-33T>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 152,086 control chromosomes in the GnomAD database, including 13,075 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. There are indicators that this mutation may affect the branch point..

• Frequency:
  • Genomes: 𝑓 0.41 (13072 hom., cov: 32)
  • Exomes 𝑓: 0.38 (3 hom.)
• Consequence: ZNF37A NM_001324250.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: This place is a probable branch point but likely benign (scored 0 / 10). Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF37A	NM_001324250.3	c.-105-33T>G		intron_variant		ENST00000685332.1	NP_001311179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF37A	ENST00000685332.1	c.-105-33T>G		intron_variant			NM_001324250.3	ENSP00000508865.1
PLD5P1	ENST00000640275.1	n.-105-33T>G		intron_variant		5		ENSP00000491560.1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62493 AN: 151928 Hom.: 13038 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.427

GnomAD4 exome AF: 0.375 AC: 15 AN: 40 Hom.: 3 Cov.: 0 AF XY: 0.292 AC XY: 7 AN XY: 24

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.412 AC: 62581 AN: 152046 Hom.: 13072 Cov.: 32 AF XY: 0.407 AC XY: 30247 AN XY: 74344

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.426

Alfa AF: 0.414 Hom.: 1625

Bravo AF: 0.430

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.54
BranchPoint Hunter		0.0
RBP_binding_hub_radar		0.91
RBP_regulation_power_radar		2.2

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: rs2474571; hg19: chr10-38384639;