rs7250240

chr19-53419262-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ZNF765-ZNF761 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF765-ZNF761	NM_001350496.2	c.-1344-3800G>T		intron_variant
ZNF765	NR_146721.2	n.261-3800G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF765	ENST00000504235.5	c.143-3800G>T		intron_variant, NMD_transcript_variant		1
ZNF765	ENST00000594030.2	c.143-3800G>T		intron_variant		4
ZNF765	ENST00000507045.5	c.16-3800G>T		intron_variant, NMD_transcript_variant		2
ZNF765	ENST00000504146.5	n.506-3800G>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.172

Alfa AF: 0.168 Hom.: 1201

Bravo AF: 0.170

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.61
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7250240; hg19: chr19-53922515;