rs10490481

Positions:

• chr2-15079920-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017004317.2(NBAS):​c.*48+57436A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,230 control chromosomes in the GnomAD database, including 3,784 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 0.14 (3784 hom., cov: 32)
• Consequence: NBAS XM_017004317.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

NBAS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBAS	XM_017004317.2	c.*48+57436A>C		intron_variant			XP_016859806.1
NBAS	XR_007076390.1	n.7015+3945A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20718 AN: 152112 Hom.: 3757 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00604

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.137 AC: 20793 AN: 152230 Hom.: 3784 Cov.: 32 AF XY: 0.136 AC XY: 10135 AN XY: 74444

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0101

Gnomad4 FIN AF: 0.0207

Gnomad4 NFE AF: 0.00604

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0585 Hom.: 318

Bravo AF: 0.160

Asia WGS AF: 0.0810 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490481; hg19: chr2-15220044;