10-38127461-C-T

Variant names:

• chr10-38127461-C-T
• rs2474584
• ENST00000640275.1:n.238+12171C>T

Variant summary

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

The ENST00000640275.1(PLD5P1):​n.238+12171C>T 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 151,946 control chromosomes in the GnomAD database, including 13,068 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 (13068 hom., cov: 32)
• Consequence: PLD5P1 ENST00000640275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 8 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 = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF37A	NM_001324256.2	c.238+12171C>T		intron_variant	Intron 7 of 7		NP_001311185.1
ZNF37A	NM_001324257.2	c.238+12171C>T		intron_variant	Intron 7 of 7		NP_001311186.1
ZNF37A	NM_001324258.2	c.238+12171C>T		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+12171C>T		intron_variant	Intron 7 of 17	5		ENSP00000491560.1
ZNF37A	ENST00000638053.1	c.238+12171C>T		intron_variant	Intron 7 of 7	5		ENSP00000490669.1
ENSG00000302873	ENST00000790161.1	n.343+29648G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62477 AN: 151828 Hom.: 13034 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.497

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

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

GnomAD4 genome AF: 0.412 AC: 62565 AN: 151946 Hom.: 13068 Cov.: 32 AF XY: 0.407 AC XY: 30225 AN XY: 74254

African (AFR) AF: 0.416 AC: 17212 AN: 41418

American (AMR) AF: 0.467 AC: 7133 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2579 AN: 5174

South Asian (SAS) AF: 0.249 AC: 1200 AN: 4820

European-Finnish (FIN) AF: 0.315 AC: 3315 AN: 10530

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

European-Non Finnish (NFE) AF: 0.418 AC: 28409 AN: 67942

Other (OTH) AF: 0.425 AC: 896 AN: 2108

Alfa AF: 0.288 Hom.: 737

Bravo AF: 0.430

Asia WGS AF: 0.406 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.31
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs2474584; hg19: chr10-38416389;