NM_001277403.2:c.4-6940T>C

Variant names:

• chr19-23127140-T-C
• rs8812
• NM_001277403.2:c.4-6940T>C

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 publications found

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)

LOC100419307 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277403.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF730	NM_001277403.2	MANE Select	c.4-6940T>C		intron	N/A	NP_001264332.1	Q6ZMV8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF730	ENST00000597761.7	TSL:5 MANE Select	c.4-6940T>C		intron	N/A	ENSP00000472959.1	Q6ZMV8
	ZNF730	ENST00000593635.1	TSL:3	c.-93-6940T>C		intron	N/A	ENSP00000469853.1	M0QYI4
	SNX6P1	ENST00000601728.1	TSL:6	n.653A>G		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.00 AC: 0 AN: 10100

American (AMR) AF: 0.00 AC: 0 AN: 25556

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11248

East Asian (EAS) AF: 0.0000660 AC: 1 AN: 15142

South Asian (SAS) AF: 0.0000344 AC: 2 AN: 58198

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27202

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1944

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 196302

Other (OTH) AF: 0.00 AC: 0 AN: 17478

GnomAD4 genome Cov.: 33

Alfa AF: 0.188 Hom.: 138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.4
DANN	Benign	0.31
PhyloP100		0.81

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: rs8812; hg19: chr19-23309942;