rs7018449

Variant names:

• chr8-80664730-T-C
• rs7018449
• NM_001033723.3:c.927+85A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-80664730-T-C
• chr8-80664730-T-G

Variant summary

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

The NM_001033723.3(ZNF704):​c.927+85A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0763 in 1,535,786 control chromosomes in the GnomAD database, including 8,639 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 0.15 (3359 hom., cov: 32)
  • Exomes 𝑓: 0.068 (5280 hom.)
• Consequence: ZNF704 NM_001033723.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 5 publications found

Genes affected

ZNF704 (HGNC:32291): (zinc finger protein 704) Enables sequence-specific double-stranded 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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF704	NM_001033723.3	c.927+85A>G		intron_variant	Intron 6 of 8	ENST00000327835.7	NP_001028895.1
ZNF704	NM_001367783.1	c.1449+85A>G		intron_variant	Intron 6 of 8		NP_001354712.1
ZNF704	XM_017013725.2	c.951+85A>G		intron_variant	Intron 6 of 8		XP_016869214.1
ZNF704	XR_928797.3	n.1873+85A>G		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF704	ENST00000327835.7	c.927+85A>G		intron_variant	Intron 6 of 8	1	NM_001033723.3	ENSP00000331462.3
ZNF704	ENST00000519936.2	c.1449+85A>G		intron_variant	Intron 6 of 8	5		ENSP00000427715.2
ZNF704	ENST00000522040.5	n.*112A>G		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23097 AN: 152096 Hom.: 3340 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0597

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.0680 AC: 94054 AN: 1383574 Hom.: 5280 AF XY: 0.0659 AC XY: 45284 AN XY: 686966

African (AFR) AF: 0.396 AC: 12383 AN: 31296

American (AMR) AF: 0.0560 AC: 2301 AN: 41078

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 2137 AN: 23528

East Asian (EAS) AF: 0.000358 AC: 14 AN: 39076

South Asian (SAS) AF: 0.0181 AC: 1439 AN: 79566

European-Finnish (FIN) AF: 0.0583 AC: 3032 AN: 52006

Middle Eastern (MID) AF: 0.0882 AC: 444 AN: 5036

European-Non Finnish (NFE) AF: 0.0642 AC: 67701 AN: 1054768

Other (OTH) AF: 0.0804 AC: 4603 AN: 57220

GnomAD4 genome AF: 0.152 AC: 23157 AN: 152212 Hom.: 3359 Cov.: 32 AF XY: 0.147 AC XY: 10964 AN XY: 74420

African (AFR) AF: 0.385 AC: 15979 AN: 41488

American (AMR) AF: 0.0819 AC: 1252 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5192

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4826

European-Finnish (FIN) AF: 0.0597 AC: 634 AN: 10612

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0661 AC: 4493 AN: 68018

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.0920 Hom.: 3889

Bravo AF: 0.162

Asia WGS AF: 0.0310 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.026
DANN	Benign	0.45
PhyloP100		-2.7
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: rs7018449; hg19: chr8-81576965;