22-36855968-A-G

Position:

• chr22-36855968-A-G

Variant summary

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

The ENST00000619915.1(NCF4-AS1):​n.350-7951T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,792 control chromosomes in the GnomAD database, including 12,722 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 0.37 (12722 hom., cov: 31)
• Consequence: NCF4-AS1 ENST00000619915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

Genes affected

NCF4-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1	n.352-7951T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCF4-AS1	ENST00000619915.1	n.350-7951T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56420 AN: 151674 Hom.: 12711 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.372 AC: 56439 AN: 151792 Hom.: 12722 Cov.: 31 AF XY: 0.385 AC XY: 28539 AN XY: 74154

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.361

Alfa AF: 0.418 Hom.: 27990

Bravo AF: 0.353

Asia WGS AF: 0.517 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.7
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10854693; hg19: chr22-37252010;