XR_928444.3:n.662+6794C>T

Variant names:

• chr8-98186838-C-T
• rs896416
• XR_928444.3:n.662+6794C>T

Variant summary

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

The XR_928444.3(NIPAL2-AS1):​n.662+6794C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,888 control chromosomes in the GnomAD database, including 17,011 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 0.47 (17011 hom., cov: 31)
• Consequence: NIPAL2-AS1 XR_928444.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 4 publications found

Genes affected

NIPAL2-AS1 (HGNC:56271): (NIPAL2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71412 AN: 151770 Hom.: 16997 Cov.: 31

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.471 AC: 71470 AN: 151888 Hom.: 17011 Cov.: 31 AF XY: 0.476 AC XY: 35355 AN XY: 74202

African (AFR) AF: 0.480 AC: 19897 AN: 41422

American (AMR) AF: 0.532 AC: 8115 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3466

East Asian (EAS) AF: 0.593 AC: 3058 AN: 5160

South Asian (SAS) AF: 0.591 AC: 2836 AN: 4800

European-Finnish (FIN) AF: 0.466 AC: 4909 AN: 10536

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29346 AN: 67938

Other (OTH) AF: 0.461 AC: 970 AN: 2104

Alfa AF: 0.446 Hom.: 48959

Bravo AF: 0.472

Asia WGS AF: 0.594 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs896416; hg19: chr8-99199066;