chr10-38128265-T-C

Variant names:

• chr10-38128265-T-C
• rs1548255
• ENST00000640275.1:n.238+12975T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000640275.1(PLD5P1):​n.238+12975T>C 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 151,984 control chromosomes in the GnomAD database, including 13,061 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 (13061 hom., cov: 32)
• Consequence: PLD5P1 ENST00000640275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 16 publications found

Genes affected

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

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]

ZNF37A Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000302873 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640275.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF37A	NM_001324256.2		c.238+12975T>C		intron	N/A	NP_001311185.1
	ZNF37A	NM_001324257.2		c.238+12975T>C		intron	N/A	NP_001311186.1
	ZNF37A	NM_001324258.2		c.238+12975T>C		intron	N/A	NP_001311187.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5P1	ENST00000640275.1	TSL:5	n.238+12975T>C		intron	N/A	ENSP00000491560.1
	ZNF37A	ENST00000638053.1	TSL:5	c.238+12975T>C		intron	N/A	ENSP00000490669.1
	ENSG00000302873	ENST00000790161.1		n.343+28844A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62466 AN: 151866 Hom.: 13027 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.412 AC: 62554 AN: 151984 Hom.: 13061 Cov.: 32 AF XY: 0.407 AC XY: 30216 AN XY: 74266

African (AFR) AF: 0.415 AC: 17186 AN: 41436

American (AMR) AF: 0.467 AC: 7135 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2580 AN: 5162

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4818

European-Finnish (FIN) AF: 0.314 AC: 3314 AN: 10550

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28418 AN: 67952

Other (OTH) AF: 0.425 AC: 896 AN: 2106

Alfa AF: 0.420 Hom.: 17268

Bravo AF: 0.430

Asia WGS AF: 0.408 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.60
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1548255; hg19: chr10-38417193;