chr22-36856876-C-T

Variant names:

• chr22-36856876-C-T
• rs4821542
• ENST00000431290.2:n.1762G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431290.2(NCF4-AS1):​n.1762G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,088 control chromosomes in the GnomAD database, including 3,756 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 0.20 (3756 hom., cov: 33)
• Consequence: NCF4-AS1 ENST00000431290.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1	n.352-8859G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCF4-AS1	ENST00000431290.2	n.1762G>A		non_coding_transcript_exon_variant	Exon 2 of 2	3
NCF4-AS1	ENST00000805864.1	n.1859G>A		non_coding_transcript_exon_variant	Exon 2 of 2
NCF4-AS1	ENST00000619915.2	n.381-8859G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30023 AN: 151970 Hom.: 3751 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.198 AC: 30052 AN: 152088 Hom.: 3756 Cov.: 33 AF XY: 0.195 AC XY: 14512 AN XY: 74360

African (AFR) AF: 0.349 AC: 14471 AN: 41424

American (AMR) AF: 0.178 AC: 2721 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3468

East Asian (EAS) AF: 0.141 AC: 733 AN: 5184

South Asian (SAS) AF: 0.179 AC: 865 AN: 4820

European-Finnish (FIN) AF: 0.0635 AC: 672 AN: 10584

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9238 AN: 67992

Other (OTH) AF: 0.224 AC: 473 AN: 2114

Alfa AF: 0.159 Hom.: 2866

Bravo AF: 0.213

Asia WGS AF: 0.183 AC: 633 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	0.39
DANN	Benign	0.74
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4821542; hg19: chr22-37252918;