8-98186838-C-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIPAL2-AS1	XR_928444.3	n.662+6794C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;