2-15062556-A-G

Position:

• chr2-15062556-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_017004317.2(NBAS):​c.*49-64332T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,050 control chromosomes in the GnomAD database, including 21,893 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 0.51 (21893 hom., cov: 32)
• Consequence: NBAS XM_017004317.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50

Genes affected

NBAS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NBAS	XM_017004317.2	c.*49-64332T>C		intron_variant
NBAS	XR_007076390.1	n.7015+21309T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77247 AN: 151932 Hom.: 21893 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.508 AC: 77258 AN: 152050 Hom.: 21893 Cov.: 32 AF XY: 0.511 AC XY: 38002 AN XY: 74306

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.548

Alfa AF: 0.513 Hom.: 3644

Bravo AF: 0.494

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	21
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862110; hg19: chr2-15202680;