rs13503

Variant names:

• chr10-37950915-C-A
• rs13503
• ENST00000374633.5:n.2813G>T

Variant summary

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

The ENST00000374633.5(ZNF25):​n.2813G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,954 control chromosomes in the GnomAD database, including 21,422 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 0.53 (21422 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ZNF25 ENST00000374633.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 10 publications found

Genes affected

ZNF25 (HGNC:13043): (zinc finger protein 25) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF25	NM_145011.4	c.*1212G>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000302609.8	NP_659448.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF25	ENST00000374633.5	n.2813G>T		non_coding_transcript_exon_variant	Exon 7 of 7	1
ZNF25	ENST00000302609.8	c.*1212G>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_145011.4	ENSP00000302222.7

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80036 AN: 151838 Hom.: 21416 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.512

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.527 AC: 80062 AN: 151954 Hom.: 21422 Cov.: 31 AF XY: 0.534 AC XY: 39646 AN XY: 74242

African (AFR) AF: 0.491 AC: 20358 AN: 41428

American (AMR) AF: 0.480 AC: 7327 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3466

East Asian (EAS) AF: 0.444 AC: 2290 AN: 5158

South Asian (SAS) AF: 0.708 AC: 3410 AN: 4814

European-Finnish (FIN) AF: 0.681 AC: 7195 AN: 10562

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35785 AN: 67944

Other (OTH) AF: 0.513 AC: 1081 AN: 2108

Alfa AF: 0.522 Hom.: 8012

Bravo AF: 0.503

Asia WGS AF: 0.534 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.012
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13503; hg19: chr10-38239843;