rs10938799

Variant names:

• chr4-10441801-G-A
• rs10938799
• NM_053042.3:c.*1303C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-10441801-G-A
• chr4-10441801-G-T

Variant summary

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

The NM_053042.3(ZNF518B):​c.*1303C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,252 control chromosomes in the GnomAD database, including 3,897 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 0.22 (3896 hom., cov: 33)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: ZNF518B NM_053042.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 6 publications found

Genes affected

ZNF518B (HGNC:29365): (zinc finger protein 518B) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF518B Gene-Disease associations (from GenCC):

• schizophrenia

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF518B	NM_053042.3	c.*1303C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000326756.4	NP_444270.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF518B	ENST00000326756.4	c.*1303C>T		3_prime_UTR_variant	Exon 3 of 3	3	NM_053042.3	ENSP00000317614.3

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32859 AN: 152092 Hom.: 3899 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.310 AC: 13 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.281 AC XY: 9 AN XY: 32

African (AFR) AF: 0.500 AC: 1 AN: 2

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) AF: 0.289 AC: 11 AN: 38

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.216 AC: 32861 AN: 152210 Hom.: 3896 Cov.: 33 AF XY: 0.219 AC XY: 16320 AN XY: 74416

African (AFR) AF: 0.114 AC: 4718 AN: 41532

American (AMR) AF: 0.275 AC: 4202 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 897 AN: 3472

East Asian (EAS) AF: 0.193 AC: 1002 AN: 5180

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4828

European-Finnish (FIN) AF: 0.306 AC: 3234 AN: 10582

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17018 AN: 68006

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.241 Hom.: 3373

Bravo AF: 0.210

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.30
PhyloP100		-0.21
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: rs10938799; hg19: chr4-10443425;