rs1883112

chr22-36860804-G-Achr22-36860804-G-Cchr22-36860804-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_147197.1(NCF4-AS1):n.351+9289C>T 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 0.395 in 151,916 control chromosomes in the GnomAD database, including 13,554 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.40 (13554 hom., cov: 31)
• Consequence: NCF4-AS1 NR_147197.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.793

Genes affected

NCF4-AS1 (HGNC:40393): (NCF4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 22-36860804-G-A is Benign according to our data. Variant chr22-36860804-G-A is described in ClinVar as [Benign]. Clinvar id is 1270928.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCF4-AS1	NR_147197.1	n.351+9289C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCF4-AS1	ENST00000619915.1	n.349+9289C>T		intron_variant, non_coding_transcript_variant		4
NCF4-AS1	ENST00000431290.1	n.289-2561C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59998 AN: 151796 Hom.: 13538 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.395 AC: 60026 AN: 151916 Hom.: 13554 Cov.: 31 AF XY: 0.407 AC XY: 30190 AN XY: 74232

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.382

Alfa AF: 0.436 Hom.: 8840

Bravo AF: 0.378

Asia WGS AF: 0.536 AC: 1864 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	12
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883112; hg19: chr22-37256846;