1-46377860-T-C

Position:

• chr1-46377860-T-C

Variant summary

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

The NM_001387270.1(NSUN4):​c.879-5976T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,912 control chromosomes in the GnomAD database, including 13,879 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 0.42 (13879 hom., cov: 31)
• Consequence: NSUN4 NM_001387270.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

NSUN4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NSUN4	NM_001387270.1	c.879-5976T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64345 AN: 151794 Hom.: 13843 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.424 AC: 64416 AN: 151912 Hom.: 13879 Cov.: 31 AF XY: 0.422 AC XY: 31329 AN XY: 74242

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.426

Alfa AF: 0.416 Hom.: 1992

Bravo AF: 0.418

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12073998; hg19: chr1-46843532;