22-36853449-G-C

Variant names:

• chr22-36853449-G-C
• rs5756372
• ENST00000619915.2:n.381-5432C>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.381-5432C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,056 control chromosomes in the GnomAD database, including 53,114 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 0.83 (53114 hom., cov: 30)
• Consequence: NCF4-AS1 ENST00000619915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1	n.352-5432C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCF4-AS1	ENST00000619915.2	n.381-5432C>G		intron_variant	Intron 1 of 1	4
NCF4-AS1	ENST00000805861.1	n.355-5432C>G		intron_variant	Intron 1 of 2
NCF4-AS1	ENST00000805862.1	n.609+2863C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126356 AN: 151938 Hom.: 53053 Cov.: 30

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.832 AC: 126476 AN: 152056 Hom.: 53114 Cov.: 30 AF XY: 0.830 AC XY: 61716 AN XY: 74314

African (AFR) AF: 0.945 AC: 39233 AN: 41504

American (AMR) AF: 0.862 AC: 13168 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2904 AN: 3468

East Asian (EAS) AF: 0.905 AC: 4672 AN: 5160

South Asian (SAS) AF: 0.812 AC: 3905 AN: 4812

European-Finnish (FIN) AF: 0.716 AC: 7552 AN: 10554

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52361 AN: 67972

Other (OTH) AF: 0.837 AC: 1765 AN: 2108

Alfa AF: 0.770 Hom.: 2697

Bravo AF: 0.848

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs5756372; hg19: chr22-37249491;