rs9680849

Variant names:

• chr22-36854415-T-A
• rs9680849
• ENST00000619915.2:n.381-6398A>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.381-6398A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,894 control chromosomes in the GnomAD database, including 3,491 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 (3491 hom., cov: 32)
• Consequence: NCF4-AS1 ENST00000619915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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.352-6398A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF4-AS1	ENST00000619915.2	TSL:4	n.381-6398A>T		intron	N/A
	NCF4-AS1	ENST00000805861.1		n.355-6398A>T		intron	N/A
	NCF4-AS1	ENST00000805862.1		n.609+1897A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25544 AN: 151778 Hom.: 3480 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.168 AC: 25589 AN: 151894 Hom.: 3491 Cov.: 32 AF XY: 0.166 AC XY: 12292 AN XY: 74272

African (AFR) AF: 0.372 AC: 15361 AN: 41252

American (AMR) AF: 0.137 AC: 2098 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3466

East Asian (EAS) AF: 0.0710 AC: 368 AN: 5182

South Asian (SAS) AF: 0.113 AC: 544 AN: 4818

European-Finnish (FIN) AF: 0.0465 AC: 492 AN: 10584

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0832 AC: 5658 AN: 67996

Other (OTH) AF: 0.167 AC: 351 AN: 2108

Alfa AF: 0.135 Hom.: 278

Bravo AF: 0.183

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.84
PhyloP100		-0.21

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: rs9680849;

hg19: chr22-37250457;