NM_152411.4:c.19-1591G>A

Variant names:

• chr7-149082308-C-T
• rs1405123
• NM_152411.4:c.19-1591G>A

Variant summary

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

The NM_152411.4(ZNF786):​c.19-1591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,146 control chromosomes in the GnomAD database, including 49,882 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 0.81 (49882 hom., cov: 32)
• Consequence: ZNF786 NM_152411.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 10 publications found

Genes affected

ZNF786 (HGNC:21806): (zinc finger protein 786) Predicted to enable DNA-binding transcription activator 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. 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF786	NM_152411.4	c.19-1591G>A		intron_variant	Intron 1 of 3	ENST00000491431.2	NP_689624.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF786	ENST00000491431.2	c.19-1591G>A		intron_variant	Intron 1 of 3	1	NM_152411.4	ENSP00000417470.1
ZNF786	ENST00000316286.13	c.-113-7770G>A		intron_variant	Intron 1 of 2	1		ENSP00000313516.9

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122877 AN: 152028 Hom.: 49841 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.808 AC: 122972 AN: 152146 Hom.: 49882 Cov.: 32 AF XY: 0.816 AC XY: 60700 AN XY: 74380

African (AFR) AF: 0.771 AC: 31968 AN: 41480

American (AMR) AF: 0.848 AC: 12958 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2792 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4952 AN: 5184

South Asian (SAS) AF: 0.910 AC: 4394 AN: 4828

European-Finnish (FIN) AF: 0.871 AC: 9220 AN: 10590

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54035 AN: 68002

Other (OTH) AF: 0.798 AC: 1687 AN: 2114

Alfa AF: 0.793 Hom.: 62965

Bravo AF: 0.801

Asia WGS AF: 0.927 AC: 3222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.74
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1405123; hg19: chr7-148779400;