rs7239368

Variant names:

• chr18-34065415-G-A
• rs7239368
• NM_003787.5:c.772+28050C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-34065415-G-A
• chr18-34065415-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003787.5(NOL4):​c.772+28050C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,654 control chromosomes in the GnomAD database, including 11,635 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 (11635 hom., cov: 32)
• Consequence: NOL4 NM_003787.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 14 publications found

Genes affected

NOL4 (HGNC:7870): (nucleolar protein 4) Predicted to enable RNA binding activity. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOL4	NM_003787.5	c.772+28050C>T		intron_variant	Intron 5 of 10	ENST00000261592.10	NP_003778.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOL4	ENST00000261592.10	c.772+28050C>T		intron_variant	Intron 5 of 10	1	NM_003787.5	ENSP00000261592.4

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58117 AN: 151534 Hom.: 11639 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.383 AC: 58116 AN: 151654 Hom.: 11635 Cov.: 32 AF XY: 0.385 AC XY: 28549 AN XY: 74096

African (AFR) AF: 0.273 AC: 11298 AN: 41406

American (AMR) AF: 0.359 AC: 5468 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3466

East Asian (EAS) AF: 0.527 AC: 2718 AN: 5160

South Asian (SAS) AF: 0.533 AC: 2567 AN: 4818

European-Finnish (FIN) AF: 0.414 AC: 4372 AN: 10564

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28916 AN: 67682

Other (OTH) AF: 0.392 AC: 828 AN: 2110

Alfa AF: 0.411 Hom.: 24764

Bravo AF: 0.371

Asia WGS AF: 0.504 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	13
DANN	Benign	0.57
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7239368; hg19: chr18-31645379;