rs730483

Variant names:

• chr22-36851836-C-A
• rs730483
• ENST00000619915.2:n.381-3819G>T

Variant summary

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

The ENST00000619915.2(NCF4-AS1):​n.381-3819G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,222 control chromosomes in the GnomAD database, including 1,529 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 0.13 (1529 hom., cov: 33)
• Consequence: NCF4-AS1 ENST00000619915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 7 publications found

Genes affected

NCF4-AS1 (HGNC:40393): (NCF4 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619915.2. 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
	NCF4-AS1	NR_147197.1		n.352-3819G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF4-AS1	ENST00000619915.2	TSL:4	n.381-3819G>T		intron	N/A
	NCF4-AS1	ENST00000805861.1		n.355-3819G>T		intron	N/A
	NCF4-AS1	ENST00000805862.1		n.610-3819G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20231 AN: 152104 Hom.: 1530 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.133 AC: 20238 AN: 152222 Hom.: 1529 Cov.: 33 AF XY: 0.132 AC XY: 9831 AN XY: 74432

African (AFR) AF: 0.205 AC: 8513 AN: 41514

American (AMR) AF: 0.122 AC: 1862 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3470

East Asian (EAS) AF: 0.0687 AC: 356 AN: 5180

South Asian (SAS) AF: 0.0740 AC: 357 AN: 4826

European-Finnish (FIN) AF: 0.107 AC: 1131 AN: 10618

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7153 AN: 68004

Other (OTH) AF: 0.144 AC: 305 AN: 2112

Alfa AF: 0.111 Hom.: 2261

Bravo AF: 0.136

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.67
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs730483;

hg19: chr22-37247878;