rs736191

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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 v4.9

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;