7-127420242-T-C

Position:

• chr7-127420242-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439506.1(ZNF800):​c.-59+11627A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,208 control chromosomes in the GnomAD database, including 3,774 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 0.21 (3774 hom., cov: 33)
• Consequence: ZNF800 ENST00000439506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127420242T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF800	ENST00000439506.1	c.-59+11627A>G		intron_variant		1		ENSP00000389776.1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32019 AN: 152090 Hom.: 3775 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.210 AC: 32022 AN: 152208 Hom.: 3774 Cov.: 33 AF XY: 0.209 AC XY: 15519 AN XY: 74428

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.0705

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.216

Alfa AF: 0.132 Hom.: 313

Bravo AF: 0.212

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11563330; hg19: chr7-127060296;