ENST00000619915.2:n.381-7951T>C

Variant names:

• chr22-36855968-A-G
• rs10854693
• ENST00000619915.2:n.381-7951T>C

Variant summary

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

The ENST00000619915.2(NCF4-AS1):​n.381-7951T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,792 control chromosomes in the GnomAD database, including 12,722 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 0.37 (12722 hom., cov: 31)
• Consequence: NCF4-AS1 ENST00000619915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• 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=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1	n.352-7951T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCF4-AS1	ENST00000619915.2	n.381-7951T>C		intron_variant	Intron 1 of 1	4
NCF4-AS1	ENST00000805861.1	n.355-7951T>C		intron_variant	Intron 1 of 2
NCF4-AS1	ENST00000805862.1	n.609+344T>C		intron_variant	Intron 2 of 2
NCF4-AS1	ENST00000805863.1	n.*72T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56420 AN: 151674 Hom.: 12711 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.372 AC: 56439 AN: 151792 Hom.: 12722 Cov.: 31 AF XY: 0.385 AC XY: 28539 AN XY: 74154

African (AFR) AF: 0.123 AC: 5102 AN: 41414

American (AMR) AF: 0.482 AC: 7357 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3387 AN: 5136

South Asian (SAS) AF: 0.463 AC: 2223 AN: 4798

European-Finnish (FIN) AF: 0.609 AC: 6396 AN: 10506

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29580 AN: 67906

Other (OTH) AF: 0.361 AC: 759 AN: 2104

Alfa AF: 0.412 Hom.: 58164

Bravo AF: 0.353

Asia WGS AF: 0.517 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.7
DANN	Benign	0.90
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs10854693; hg19: chr22-37252010;