9-68299062-C-T

Variant names:

• chr9-68299062-C-T
• rs782289490
• NM_201453.4:c.1050C>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_201453.4(ZNG1C):​c.1050C>T​(p.Asp350Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.0000066 (0 hom., cov: 21)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNG1C NM_201453.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 0 publications found

Genes affected

ZNG1C (HGNC:18519): (Zn regulated GTPase metalloprotein activator 1C) Predicted to enable ATP binding activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000300460 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP7: Synonymous conserved (PhyloP=0.366 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201453.4. 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
	ZNG1C	NM_201453.4	MANE Select	c.1050C>T	p.Asp350Asp	synonymous	Exon 14 of 15	NP_958861.2	Q5JTY5-1
	ZNG1C	NM_001291821.2		c.990C>T	p.Asp330Asp	synonymous	Exon 13 of 14	NP_001278750.1	Q5JTY5-2
	ZNG1C	NM_001378113.1		c.981C>T	p.Asp327Asp	synonymous	Exon 13 of 14	NP_001365042.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNG1C	ENST00000360171.11	TSL:1 MANE Select	c.1050C>T	p.Asp350Asp	synonymous	Exon 14 of 15	ENSP00000353295.6	Q5JTY5-1
	ZNG1C	ENST00000377342.9	TSL:1	c.993C>T	p.Asp331Asp	synonymous	Exon 13 of 14	ENSP00000366559.6	A0A0A0MRU4
	ZNG1C	ENST00000618217.4	TSL:1	c.906C>T	p.Asp302Asp	synonymous	Exon 12 of 13	ENSP00000480203.1	A0A087WWG3

Frequencies

GnomAD3 genomes AF: 0.00000660 AC: 1 AN: 151422 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.0000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.86e-7 AC: 1 AN: 1458748 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 725634

African (AFR) AF: 0.0000300 AC: 1 AN: 33368

American (AMR) AF: 0.00 AC: 0 AN: 44448

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26092

East Asian (EAS) AF: 0.00 AC: 0 AN: 39676

South Asian (SAS) AF: 0.00 AC: 0 AN: 85978

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53390

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4132

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111502

Other (OTH) AF: 0.00 AC: 0 AN: 60162

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000660 AC: 1 AN: 151422 Hom.: 0 Cov.: 21 AF XY: 0.0000135 AC XY: 1 AN XY: 73888

African (AFR) AF: 0.0000243 AC: 1 AN: 41178

American (AMR) AF: 0.00 AC: 0 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4778

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10538

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67796

Other (OTH) AF: 0.00 AC: 0 AN: 2076

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.1
DANN	Benign	0.88
PhyloP100		0.37

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: rs782289490; hg19: chr9-70913978;