rs13239338

Variant names:

• chr7-127344319-C-A
• rs13239338
• NM_001438587.1:c.*3538G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-127344319-C-A
• chr7-127344319-C-T

Variant summary

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

The NM_001438587.1(ZNF800):​c.*3538G>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 0.104 in 151,956 control chromosomes in the GnomAD database, including 1,068 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 0.10 (1068 hom., cov: 33)
• Consequence: ZNF800 NM_001438587.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 3 publications found

Genes affected

ZNF800 (HGNC:27267): (zinc finger protein 800) Predicted to enable DNA binding activity and metal ion binding activity. 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF800	NM_001438587.1	c.*3538G>T		3_prime_UTR_variant	Exon 6 of 6		NP_001425516.1
ZNF800	NM_001438588.1	c.*3538G>T		3_prime_UTR_variant	Exon 5 of 5		NP_001425517.1
ZNF800	NM_001438611.1	c.*3342G>T		3_prime_UTR_variant	Exon 6 of 6		NP_001425540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15870 AN: 151838 Hom.: 1068 Cov.: 33

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.104 AC: 15858 AN: 151956 Hom.: 1068 Cov.: 33 AF XY: 0.105 AC XY: 7786 AN XY: 74256

African (AFR) AF: 0.0301 AC: 1251 AN: 41534

American (AMR) AF: 0.103 AC: 1573 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3472

East Asian (EAS) AF: 0.0686 AC: 355 AN: 5176

South Asian (SAS) AF: 0.0912 AC: 440 AN: 4826

European-Finnish (FIN) AF: 0.169 AC: 1786 AN: 10552

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.131 AC: 8897 AN: 67812

Other (OTH) AF: 0.129 AC: 271 AN: 2104

Alfa AF: 0.0397 Hom.: 37

Bravo AF: 0.0975

Asia WGS AF: 0.0770 AC: 268 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.50
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs13239338; hg19: chr7-126984373;