rs7790549

Variant names:

• chr7-150392944-A-G
• rs7790549
• NM_173680.4:c.32-3569A>G

Variant summary

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

The NM_173680.4(ZNF775):​c.32-3569A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,268 control chromosomes in the GnomAD database, including 61,574 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 0.90 (61574 hom., cov: 32)
• Consequence: ZNF775 NM_173680.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 5 publications found

Genes affected

ZNF775 (HGNC:28501): (zinc finger protein 775) 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]

ENSG00000284048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF775	NM_173680.4	c.32-3569A>G		intron_variant	Intron 2 of 2	ENST00000329630.10	NP_775951.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF775	ENST00000329630.10	c.32-3569A>G		intron_variant	Intron 2 of 2	1	NM_173680.4	ENSP00000330838.5

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136650 AN: 152150 Hom.: 61527 Cov.: 32

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.898 AC: 136751 AN: 152268 Hom.: 61574 Cov.: 32 AF XY: 0.894 AC XY: 66538 AN XY: 74456

African (AFR) AF: 0.898 AC: 37316 AN: 41536

American (AMR) AF: 0.895 AC: 13698 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2876 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3993 AN: 5184

South Asian (SAS) AF: 0.791 AC: 3821 AN: 4830

European-Finnish (FIN) AF: 0.876 AC: 9276 AN: 10586

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62773 AN: 68036

Other (OTH) AF: 0.876 AC: 1850 AN: 2112

Alfa AF: 0.910 Hom.: 8539

Bravo AF: 0.899

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.63
PhyloP100		-0.96
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: rs7790549; hg19: chr7-150090032;