chr7-88931564-G-C

Position:

• chr7-88931564-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_181646.5(ZNF804B):​c.108+171480G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.033 in 151,828 control chromosomes in the GnomAD database, including 102 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 0.033 (102 hom., cov: 32)
• Consequence: ZNF804B NM_181646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.033 (5007/151828) while in subpopulation EAS AF= 0.0492 (254/5166). AF 95% confidence interval is 0.0442. There are 102 homozygotes in gnomad4. There are 2572 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 102 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF804B	NM_181646.5	c.108+171480G>C		intron_variant		ENST00000333190.5	NP_857597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF804B	ENST00000333190.5	c.108+171480G>C		intron_variant		1	NM_181646.5	ENSP00000329638	P1

Frequencies

GnomAD3 genomes AF: 0.0329 AC: 4994 AN: 151710 Hom.: 100 Cov.: 32

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.0312

Gnomad EAS AF: 0.0492

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0369

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

GnomAD4 genome AF: 0.0330 AC: 5007 AN: 151828 Hom.: 102 Cov.: 32 AF XY: 0.0347 AC XY: 2572 AN XY: 74190

Gnomad4 AFR AF: 0.0210

Gnomad4 AMR AF: 0.0465

Gnomad4 ASJ AF: 0.0312

Gnomad4 EAS AF: 0.0492

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.0448

Gnomad4 NFE AF: 0.0358

Gnomad4 OTH AF: 0.0394

Alfa AF: 0.00831 Hom.: 2

Bravo AF: 0.0326

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406503; hg19: chr7-88560878;