15-90005073-G-A

Variant names:

• chr15-90005073-G-A
• rs1256841
• NM_198526.4:c.-29+3459G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198526.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF710	NM_198526.4	MANE Select	c.-29+3459G>A		intron	N/A	NP_940928.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF710	ENST00000268154.9	TSL:2 MANE Select	c.-29+3459G>A		intron	N/A	ENSP00000268154.3
	ZNF710	ENST00000559419.1	TSL:3	c.-29+2521G>A		intron	N/A	ENSP00000452993.1

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

African (AFR) AF: 0.980 AC: 40758 AN: 41584

American (AMR) AF: 0.937 AC: 14323 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3023 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5188 AN: 5192

South Asian (SAS) AF: 0.973 AC: 4694 AN: 4826

European-Finnish (FIN) AF: 0.921 AC: 9766 AN: 10606

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60035 AN: 68026

Other (OTH) AF: 0.924 AC: 1951 AN: 2112

Alfa AF: 0.896 Hom.: 97785

Bravo AF: 0.928

Asia WGS AF: 0.982 AC: 3415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.19
DANN	Benign	0.53
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1256841; hg19: chr15-90548305;