5-16451322-C-G

Variant names:

• chr5-16451322-C-G
• rs26017
• ENST00000773338.1:n.430-6259C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000773338.1(ENSG00000300672):​n.430-6259C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,096 control chromosomes in the GnomAD database, including 48,817 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 0.80 (48817 hom., cov: 31)
• Consequence: ENSG00000300672 ENST00000773338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 3 publications found

Genes affected

ENSG00000300672 (HGNC:):

ZNF622 (HGNC:30958): (zinc finger protein 622) Enables RNA binding activity. Involved in several processes, including intrinsic apoptotic signaling pathway in response to oxidative stress; positive regulation of JNK cascade; and positive regulation of kinase activity. Located in Golgi apparatus; cytosol; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF622	NM_033414.3	c.*335G>C		downstream_gene_variant		ENST00000308683.3	NP_219482.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300672	ENST00000773338.1	n.430-6259C>G		intron_variant	Intron 2 of 3
ZNF622	ENST00000308683.3	c.*335G>C		downstream_gene_variant		1	NM_033414.3	ENSP00000310042.2

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121377 AN: 151978 Hom.: 48758 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.799 AC: 121506 AN: 152096 Hom.: 48817 Cov.: 31 AF XY: 0.797 AC XY: 59263 AN XY: 74342

African (AFR) AF: 0.897 AC: 37230 AN: 41502

American (AMR) AF: 0.772 AC: 11801 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2663 AN: 3472

East Asian (EAS) AF: 0.694 AC: 3578 AN: 5156

South Asian (SAS) AF: 0.671 AC: 3235 AN: 4818

European-Finnish (FIN) AF: 0.790 AC: 8346 AN: 10558

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52060 AN: 67992

Other (OTH) AF: 0.789 AC: 1665 AN: 2110

Alfa AF: 0.743 Hom.: 2584

Bravo AF: 0.803

Asia WGS AF: 0.737 AC: 2562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.39
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs26017; hg19: chr5-16451431;