rs5995355

Variant names:

• chr22-36855419-A-G
• rs5995355
• ENST00000619915.2:n.381-7402T>C

Your query was ambiguous. Multiple possible variants found:

• chr22-36855419-A-G
• chr22-36855419-A-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.381-7402T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,252 control chromosomes in the GnomAD database, including 3,675 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 0.16 (3675 hom., cov: 33)
• Consequence: NCF4-AS1 ENST00000619915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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.352-7402T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF4-AS1	ENST00000619915.2	TSL:4	n.381-7402T>C		intron	N/A
	NCF4-AS1	ENST00000805861.1		n.355-7402T>C		intron	N/A
	NCF4-AS1	ENST00000805862.1		n.609+893T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24836 AN: 152134 Hom.: 3665 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0723

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0361

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.163 AC: 24874 AN: 152252 Hom.: 3675 Cov.: 33 AF XY: 0.160 AC XY: 11901 AN XY: 74440

African (AFR) AF: 0.391 AC: 16215 AN: 41490

American (AMR) AF: 0.132 AC: 2016 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3472

East Asian (EAS) AF: 0.0720 AC: 374 AN: 5192

South Asian (SAS) AF: 0.0853 AC: 412 AN: 4832

European-Finnish (FIN) AF: 0.0361 AC: 383 AN: 10624

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0670 AC: 4559 AN: 68018

Other (OTH) AF: 0.157 AC: 331 AN: 2114

Alfa AF: 0.0864 Hom.: 390

Bravo AF: 0.179

Asia WGS AF: 0.111 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.35
PhyloP100		0.010

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: rs5995355;

hg19: chr22-37251461;