ENST00000431290.2:n.1441G>A

Variant names:

• chr22-36857197-C-T
• rs7287350
• ENST00000431290.2:n.1441G>A

Variant summary

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

The ENST00000431290.2(NCF4-AS1):​n.1441G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 152,290 control chromosomes in the GnomAD database, including 185 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 0.045 (185 hom., cov: 33)
• Consequence: NCF4-AS1 ENST00000431290.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.0826 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431290.2. 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.352-9180G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF4-AS1	ENST00000431290.2	TSL:3	n.1441G>A		non_coding_transcript_exon	Exon 2 of 2
	NCF4-AS1	ENST00000805864.1		n.1538G>A		non_coding_transcript_exon	Exon 2 of 2
	NCF4-AS1	ENST00000619915.2	TSL:4	n.381-9180G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6875 AN: 152172 Hom.: 185 Cov.: 33

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0452 AC: 6877 AN: 152290 Hom.: 185 Cov.: 33 AF XY: 0.0429 AC XY: 3195 AN XY: 74472

African (AFR) AF: 0.0358 AC: 1489 AN: 41558

American (AMR) AF: 0.0463 AC: 708 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.0893 AC: 462 AN: 5174

South Asian (SAS) AF: 0.0350 AC: 169 AN: 4832

European-Finnish (FIN) AF: 0.0153 AC: 162 AN: 10620

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0503 AC: 3420 AN: 68016

Other (OTH) AF: 0.0586 AC: 124 AN: 2116

Alfa AF: 0.0476 Hom.: 190

Bravo AF: 0.0475

Asia WGS AF: 0.0620 AC: 214 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	0.99
DANN	Benign	0.77
PhyloP100		-0.73
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: rs7287350;

hg19: chr22-37253239;