22-36854729-G-A

Variant names:

• chr22-36854729-G-A
• rs6000448
• ENST00000619915.2:n.381-6712C>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.381-6712C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,096 control chromosomes in the GnomAD database, including 3,605 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 0.17 (3605 hom., cov: 32)
• Consequence: NCF4-AS1 ENST00000619915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF4-AS1	NR_147197.1		n.352-6712C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF4-AS1	ENST00000619915.2	TSL:4	n.381-6712C>T		intron	N/A
	NCF4-AS1	ENST00000805861.1		n.355-6712C>T		intron	N/A
	NCF4-AS1	ENST00000805862.1		n.609+1583C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25863 AN: 151978 Hom.: 3594 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.170 AC: 25909 AN: 152096 Hom.: 3605 Cov.: 32 AF XY: 0.167 AC XY: 12423 AN XY: 74352

African (AFR) AF: 0.377 AC: 15624 AN: 41414

American (AMR) AF: 0.138 AC: 2107 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3468

East Asian (EAS) AF: 0.0713 AC: 369 AN: 5176

South Asian (SAS) AF: 0.113 AC: 547 AN: 4824

European-Finnish (FIN) AF: 0.0471 AC: 500 AN: 10618

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5687 AN: 67994

Other (OTH) AF: 0.167 AC: 353 AN: 2112

Alfa AF: 0.146 Hom.: 591

Bravo AF: 0.184

Asia WGS AF: 0.122 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs6000448; hg19: chr22-37250771;