rs10957985

Positions:

• chr8-80877686-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017013725.2(ZNF704):​c.3+6473C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,048 control chromosomes in the GnomAD database, including 11,082 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 0.35 (11082 hom., cov: 32)
• Consequence: ZNF704 XM_017013725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

Genes affected

ZNF704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF704	XM_017013725.2	c.3+6473C>T		intron_variant			XP_016869214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53472 AN: 151930 Hom.: 11084 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.352 AC: 53473 AN: 152048 Hom.: 11082 Cov.: 32 AF XY: 0.354 AC XY: 26327 AN XY: 74308

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.389

Alfa AF: 0.413 Hom.: 7096

Bravo AF: 0.350

Asia WGS AF: 0.355 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10957985; hg19: chr8-81789921;