XR_928444.3:n.662+2932T>C

Variant names:

• chr8-98182976-T-C
• rs736191
• XR_928444.3:n.662+2932T>C

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+2932T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,034 control chromosomes in the GnomAD database, including 18,802 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 0.49 (18802 hom., cov: 32)
• Consequence: NIPAL2-AS1 XR_928444.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIPAL2-AS1	XR_928444.3	n.662+2932T>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75220 AN: 151916 Hom.: 18791 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.495 AC: 75255 AN: 152034 Hom.: 18802 Cov.: 32 AF XY: 0.499 AC XY: 37105 AN XY: 74326

African (AFR) AF: 0.465 AC: 19248 AN: 41434

American (AMR) AF: 0.536 AC: 8190 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2136 AN: 3470

East Asian (EAS) AF: 0.468 AC: 2418 AN: 5168

South Asian (SAS) AF: 0.677 AC: 3262 AN: 4818

European-Finnish (FIN) AF: 0.474 AC: 5016 AN: 10582

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33062 AN: 67968

Other (OTH) AF: 0.500 AC: 1054 AN: 2110

Alfa AF: 0.497 Hom.: 31580

Bravo AF: 0.492

Asia WGS AF: 0.552 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs736191; hg19: chr8-99195204;