rs132817

Positions:

• chr22-45136785-A-G

Variant summary

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

The ENST00000426282.6(NUP50-DT):​n.299-1988T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,960 control chromosomes in the GnomAD database, including 11,324 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 0.38 (11324 hom., cov: 32)
• Consequence: NUP50-DT ENST00000426282.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

NUP50-DT (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 (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP50-DT	NR_038956.1	n.299-1988T>C		intron_variant
NUP50-DT	NR_038957.1	n.274-1988T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP50-DT	ENST00000426282.6	n.299-1988T>C		intron_variant		1
NUP50-DT	ENST00000609284.2	n.313-1988T>C		intron_variant		1
NUP50-DT	ENST00000432502.1	n.89-1988T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57163 AN: 151842 Hom.: 11316 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.376 AC: 57194 AN: 151960 Hom.: 11324 Cov.: 32 AF XY: 0.379 AC XY: 28167 AN XY: 74284

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.370

Alfa AF: 0.397 Hom.: 1574

Bravo AF: 0.366

Asia WGS AF: 0.385 AC: 1341 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs132817; hg19: chr22-45532666;