7-89329211-G-C

Variant names:

• chr7-89329211-G-C
• rs1468136
• NM_181646.5:c.380+1737G>C

Variant summary

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

The NM_181646.5(ZNF804B):​c.380+1737G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,496 control chromosomes in the GnomAD database, including 4,050 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 0.22 (4050 hom., cov: 32)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 1 publications found

Genes affected

ZNF804B (HGNC:21958): (zinc finger protein 804B) Predicted to enable metal ion binding activity. 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.380+1737G>C		intron_variant	Intron 3 of 3	ENST00000333190.5	NP_857597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF804B	ENST00000333190.5	c.380+1737G>C		intron_variant	Intron 3 of 3	1	NM_181646.5	ENSP00000329638.4
ZNF804B	ENST00000611114.1	c.131+1737G>C		intron_variant	Intron 2 of 2	5		ENSP00000478506.1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33005 AN: 151378 Hom.: 4046 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.218 AC: 33014 AN: 151496 Hom.: 4050 Cov.: 32 AF XY: 0.222 AC XY: 16408 AN XY: 74018

African (AFR) AF: 0.114 AC: 4719 AN: 41424

American (AMR) AF: 0.276 AC: 4186 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 670 AN: 3456

East Asian (EAS) AF: 0.112 AC: 575 AN: 5148

South Asian (SAS) AF: 0.198 AC: 954 AN: 4808

European-Finnish (FIN) AF: 0.347 AC: 3658 AN: 10540

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17588 AN: 67656

Other (OTH) AF: 0.200 AC: 418 AN: 2094

Alfa AF: 0.232 Hom.: 540

Bravo AF: 0.208

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.47
PhyloP100		0.14
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: rs1468136; hg19: chr7-88958525;