rs9680849

chr22-36854415-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147197.1(NCF4-AS1):n.352-6398A>T variant causes a intron, non coding transcript 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 NR_147197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

Genes affected

NCF4-AS1 (HGNC:40393): (NCF4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCF4-AS1	NR_147197.1	n.352-6398A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCF4-AS1	ENST00000619915.1	n.350-6398A>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0710

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.167

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.2
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9680849; hg19: chr22-37250457;