chr19-53419262-G-T

Variant names:

• chr19-53419262-G-T
• rs7250240
• ENST00000504235.5:n.143-3800G>T

Variant summary

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

The NM_001350496.2(ZNF765-ZNF761):​c.-1344-3800G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,108 control chromosomes in the GnomAD database, including 2,181 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 0.17 (2181 hom., cov: 32)
• Consequence: ZNF765-ZNF761 NM_001350496.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 4 publications found

Genes affected

ZNF765 (HGNC:25092): (zinc finger protein 765) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-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]

ZNF765-ZNF761 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350496.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF765-ZNF761	NM_001350496.2		c.-1344-3800G>T		intron	N/A	NP_001337425.1
	ZNF765	NR_146721.2		n.261-3800G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF765	ENST00000504235.5	TSL:1	n.143-3800G>T		intron	N/A	ENSP00000424395.1	Q7L2R6-2
	ZNF765	ENST00000594030.2	TSL:4	c.143-3800G>T		intron	N/A	ENSP00000470468.1	Q7L2R6-2
	ZNF765	ENST00000504146.5	TSL:4	n.506-3800G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25311 AN: 151990 Hom.: 2181 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.166 AC: 25323 AN: 152108 Hom.: 2181 Cov.: 32 AF XY: 0.164 AC XY: 12225 AN XY: 74348

African (AFR) AF: 0.168 AC: 6962 AN: 41498

American (AMR) AF: 0.176 AC: 2686 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3472

East Asian (EAS) AF: 0.119 AC: 616 AN: 5172

South Asian (SAS) AF: 0.193 AC: 928 AN: 4814

European-Finnish (FIN) AF: 0.150 AC: 1583 AN: 10576

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11199 AN: 67992

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.168 Hom.: 1309

Bravo AF: 0.170

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.33
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7250240; hg19: chr19-53922515;