chr15-90005073-G-A

Position:

• chr15-90005073-G-A

Variant summary

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

The NM_198526.4(ZNF710):​c.-29+3459G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,310 control chromosomes in the GnomAD database, including 65,254 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 0.92 (65254 hom., cov: 33)
• Consequence: ZNF710 NM_198526.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

ZNF710 (HGNC:25352): (zinc finger protein 710) Predicted to enable DNA-binding transcription factor activity 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 located 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF710	NM_198526.4	c.-29+3459G>A		intron_variant		ENST00000268154.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF710	ENST00000268154.9	c.-29+3459G>A		intron_variant		2	NM_198526.4	P1
ZNF710	ENST00000559419.1	c.-29+2521G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140649 AN: 152192 Hom.: 65188 Cov.: 33

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.924 AC: 140774 AN: 152310 Hom.: 65254 Cov.: 33 AF XY: 0.927 AC XY: 69023 AN XY: 74458

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.924

Alfa AF: 0.892 Hom.: 75462

Bravo AF: 0.928

Asia WGS AF: 0.982 AC: 3415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.19
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1256841; hg19: chr15-90548305;