XM_047419945.1:c.*7368T>C

Variant names:

• chr7-127365970-A-G
• rs951809
• XM_047419945.1:c.*7368T>C

Variant summary

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

The XM_047419945.1(ZNF800):​c.*7368T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,072 control chromosomes in the GnomAD database, including 8,764 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 0.30 (8764 hom., cov: 32)
• Consequence: ZNF800 XM_047419945.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.10
• Publications: 4 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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF800	XM_047419945.1	c.*7368T>C		3_prime_UTR_variant	Exon 4 of 4		XP_047275901.1
ZNF800	XM_047419946.1	c.*7368T>C		3_prime_UTR_variant	Exon 4 of 4		XP_047275902.1
ZNF800	NM_001438587.1	c.1994+7372T>C		intron_variant	Intron 5 of 5		NP_001425516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF800	ENST00000485577.1	n.224+7372T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45399 AN: 151954 Hom.: 8754 Cov.: 32

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.299 AC: 45420 AN: 152072 Hom.: 8764 Cov.: 32 AF XY: 0.308 AC XY: 22930 AN XY: 74330

African (AFR) AF: 0.0754 AC: 3132 AN: 41526

American (AMR) AF: 0.370 AC: 5654 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3468

East Asian (EAS) AF: 0.746 AC: 3844 AN: 5156

South Asian (SAS) AF: 0.419 AC: 2017 AN: 4816

European-Finnish (FIN) AF: 0.436 AC: 4599 AN: 10556

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24519 AN: 67958

Other (OTH) AF: 0.286 AC: 604 AN: 2110

Alfa AF: 0.201 Hom.: 545

Bravo AF: 0.288

Asia WGS AF: 0.530 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	16
DANN	Benign	0.82
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs951809; hg19: chr7-127006024;