rs1883113

Positions:

• chr22-36856642-G-C

Variant summary

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

The NR_147197.1(NCF4-AS1):​n.352-8625C>G 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 0.147 in 152,208 control chromosomes in the GnomAD database, including 2,997 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 0.15 (2997 hom., cov: 33)
• Consequence: NCF4-AS1 NR_147197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCF4-AS1	NR_147197.1	n.352-8625C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCF4-AS1	ENST00000619915.1	n.350-8625C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22357 AN: 152090 Hom.: 2984 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0783

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.147 AC: 22399 AN: 152208 Hom.: 2997 Cov.: 33 AF XY: 0.140 AC XY: 10454 AN XY: 74420

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.0872

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.0784

Gnomad4 FIN AF: 0.0207

Gnomad4 NFE AF: 0.0657

Gnomad4 OTH AF: 0.130

Alfa AF: 0.109 Hom.: 238

Bravo AF: 0.160

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883113; hg19: chr22-37252684;