rs228606

chr11-108217120-G-T

Variant summary

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

The NM_002519.3(NPAT):c.37+5380C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,000 control chromosomes in the GnomAD database, including 11,302 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 0.36 (11302 hom., cov: 31)
• Consequence: NPAT NM_002519.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

Genes affected

NPAT (HGNC:7896): (nuclear protein, coactivator of histone transcription) Enables protein C-terminus binding activity; transcription coactivator activity; and transcription corepressor activity. Involved in positive regulation of transcription by RNA polymerase II and regulation of transcription involved in G1/S transition of mitotic cell cycle. Located in Cajal body; Gemini of coiled bodies; and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPAT	NM_002519.3	c.37+5380C>A		intron_variant		ENST00000278612.9
NPAT	NM_001321307.1	c.37+5380C>A		intron_variant
NPAT	XM_011542854.3	c.37+5380C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPAT	ENST00000278612.9	c.37+5380C>A		intron_variant		1	NM_002519.3	P1
NPAT	ENST00000531384.1	c.37+5380C>A		intron_variant, NMD_transcript_variant		5
NPAT	ENST00000610253.5	n.137+5380C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54893 AN: 151882 Hom.: 11297 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.361 AC: 54908 AN: 152000 Hom.: 11302 Cov.: 31 AF XY: 0.369 AC XY: 27378 AN XY: 74284

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.419

Alfa AF: 0.393 Hom.: 4225

Bravo AF: 0.358

Asia WGS AF: 0.475 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.59
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs228606; hg19: chr11-108087847;