rs10487035

Variant names:

• chr7-88765569-C-G
• rs10487035
• NM_181646.5:c.108+5485C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-88765569-C-G
• chr7-88765569-C-T

Variant summary

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

The NM_181646.5(ZNF804B):​c.108+5485C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 151,700 control chromosomes in the GnomAD database, including 566 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 0.070 (566 hom., cov: 33)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 0 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.108+5485C>G		intron_variant	Intron 1 of 3	ENST00000333190.5	NP_857597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF804B	ENST00000333190.5	c.108+5485C>G		intron_variant	Intron 1 of 3	1	NM_181646.5	ENSP00000329638.4

Frequencies

GnomAD3 genomes AF: 0.0701 AC: 10633 AN: 151582 Hom.: 565 Cov.: 33

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0701 AC: 10636 AN: 151700 Hom.: 566 Cov.: 33 AF XY: 0.0733 AC XY: 5436 AN XY: 74142

African (AFR) AF: 0.0875 AC: 3601 AN: 41170

American (AMR) AF: 0.127 AC: 1933 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3462

East Asian (EAS) AF: 0.279 AC: 1441 AN: 5156

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4820

European-Finnish (FIN) AF: 0.0484 AC: 511 AN: 10564

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0388 AC: 2637 AN: 67962

Other (OTH) AF: 0.0659 AC: 139 AN: 2110

Alfa AF: 0.0137 Hom.: 1

Bravo AF: 0.0786

Asia WGS AF: 0.157 AC: 545 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.56
PhyloP100		0.075
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: rs10487035; hg19: chr7-88394883;