rs1883113

Variant names:

• chr22-36856642-G-C
• rs1883113
• ENST00000619915.2:n.381-8625C>G

Variant summary

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

The ENST00000619915.2(NCF4-AS1):​n.381-8625C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,208 control chromosomes in the GnomAD database, including 2,997 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 0.15 (2997 hom., cov: 33)
• Consequence: NCF4-AS1 ENST00000619915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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.352-8625C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF4-AS1	ENST00000619915.2	TSL:4	n.381-8625C>G		intron	N/A
	NCF4-AS1	ENST00000805861.1		n.355-8625C>G		intron	N/A
	NCF4-AS1	ENST00000805862.1		n.352-73C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22357 AN: 152090 Hom.: 2984 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0783

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.147 AC: 22399 AN: 152208 Hom.: 2997 Cov.: 33 AF XY: 0.140 AC XY: 10454 AN XY: 74420

African (AFR) AF: 0.356 AC: 14782 AN: 41498

American (AMR) AF: 0.0872 AC: 1334 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3472

East Asian (EAS) AF: 0.100 AC: 518 AN: 5178

South Asian (SAS) AF: 0.0784 AC: 378 AN: 4824

European-Finnish (FIN) AF: 0.0207 AC: 220 AN: 10612

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0657 AC: 4465 AN: 68010

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.109 Hom.: 238

Bravo AF: 0.160

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.44
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism

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: rs1883113;

hg19: chr22-37252684;