1-21439960-A-C

Position:

• chr1-21439960-A-C

Variant summary

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

The XM_047432037.1(NBPF3):​c.-140+3151A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,048 control chromosomes in the GnomAD database, including 8,848 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 0.33 (8848 hom., cov: 32)
• Consequence: NBPF3 XM_047432037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27

Genes affected

NBPF3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBPF3	XM_047432037.1	c.-140+3151A>C		intron_variant			XP_047287993.1
NBPF3	XM_047432038.1	c.-140+2428A>C		intron_variant			XP_047287994.1
NBPF3	XM_047432039.1	c.-140+2428A>C		intron_variant			XP_047287995.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49839 AN: 151930 Hom.: 8835 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.328 AC: 49885 AN: 152048 Hom.: 8848 Cov.: 32 AF XY: 0.330 AC XY: 24530 AN XY: 74300

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.321

Alfa AF: 0.374 Hom.: 3402

Bravo AF: 0.311

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	4.3
DANN	Benign	0.071

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1976403; hg19: chr1-21766453;