rs5995355

Positions:

• chr22-36855419-A-G
• chr22-36855419-A-T

Variant summary

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

The NR_147197.1(NCF4-AS1):​n.352-7402T>C 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 0.163 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 NR_147197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1	n.352-7402T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCF4-AS1	ENST00000619915.1	n.350-7402T>C		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0720

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.0361

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.157

Alfa AF: 0.0584 Hom.: 98

Bravo AF: 0.179

Asia WGS AF: 0.111 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5995355; hg19: chr22-37251461;