rs8812

Positions:

• chr19-23127140-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001277403.2(ZNF730):​c.4-6940T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000826 in 363,170 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000083 (0 hom.)
• Consequence: ZNF730 NM_001277403.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814

Genes affected

ZNF730 (HGNC:32470): (zinc finger protein 730) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SNX6P1 (HGNC:41511): (sorting nexin 6 pseudogene 1)

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF730	NM_001277403.2	c.4-6940T>C		intron_variant		ENST00000597761.7	NP_001264332.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF730	ENST00000597761.7	c.4-6940T>C		intron_variant		5	NM_001277403.2	ENSP00000472959	P1
SNX6P1	ENST00000601728.1	n.653A>G		non_coding_transcript_exon_variant	1/1
	ENST00000600819.1	n.157-664T>C		intron_variant, non_coding_transcript_variant
ZNF730	ENST00000593635.1	c.-93-6940T>C		intron_variant		3		ENSP00000469853

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000826 AC: 3 AN: 363170 Hom.: 0 Cov.: 0 AF XY: 0.00000974 AC XY: 2 AN XY: 205372

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000660

Gnomad4 SAS exome AF: 0.0000344

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Alfa AF: 0.188 Hom.: 138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.4
DANN	Benign	0.31

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: rs8812; hg19: chr19-23309942;