10-38126203-G-A

Variant names:

• chr10-38126203-G-A
• rs2505179
• ENST00000640275.1:n.238+10913G>A

Variant summary

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

The ENST00000640275.1(PLD5P1):​n.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: PLD5P1 ENST00000640275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 6 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=-0.99).
• 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 rank	MANE	Protein	UniProt
ZNF37A	NM_001324256.2	c.238+10913G>A		intron_variant	Intron 7 of 7		NP_001311185.1
ZNF37A	NM_001324257.2	c.238+10913G>A		intron_variant	Intron 7 of 7		NP_001311186.1
ZNF37A	NM_001324258.2	c.238+10913G>A		intron_variant	Intron 6 of 6		NP_001311187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLD5P1	ENST00000640275.1	n.238+10913G>A		intron_variant	Intron 7 of 17	5		ENSP00000491560.1
ZNF37A	ENST00000638053.1	c.238+10913G>A		intron_variant	Intron 7 of 7	5		ENSP00000490669.1
ENSG00000302873	ENST00000790161.1	n.343+30906C>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.505 AC: 20947 AN: 41446

American (AMR) AF: 0.532 AC: 8127 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1652 AN: 3468

East Asian (EAS) AF: 0.544 AC: 2813 AN: 5170

South Asian (SAS) AF: 0.311 AC: 1498 AN: 4812

European-Finnish (FIN) AF: 0.368 AC: 3881 AN: 10558

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32879 AN: 67984

Other (OTH) AF: 0.506 AC: 1069 AN: 2114

Alfa AF: 0.488 Hom.: 3192

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2505179; hg19: chr10-38415131;