4-163148797-A-G

Position:

• chr4-163148797-A-G

Variant summary

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

The NM_138386.3(NAF1):​c.541-363T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,082 control chromosomes in the GnomAD database, including 46,141 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 0.78 (46141 hom., cov: 33)
• Consequence: NAF1 NM_138386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

Genes affected

NAF1 (HGNC:25126): (nuclear assembly factor 1 ribonucleoprotein) Enables identical protein binding activity and telomerase RNA binding activity. Involved in regulation of nucleobase-containing compound metabolic process; ribosome biogenesis; and telomerase holoenzyme complex assembly. Located in nucleoplasm. Part of sno(s)RNA-containing ribonucleoprotein complex. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAF1	NM_138386.3	c.541-363T>C		intron_variant		ENST00000274054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAF1	ENST00000274054.3	c.541-363T>C		intron_variant		1	NM_138386.3	P2
NAF1	ENST00000422287.6	c.541-363T>C		intron_variant		1		A2
NAF1	ENST00000509232.5	n.645-363T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118340 AN: 151964 Hom.: 46114 Cov.: 33

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.779 AC: 118421 AN: 152082 Hom.: 46141 Cov.: 33 AF XY: 0.782 AC XY: 58105 AN XY: 74348

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.762

Alfa AF: 0.775 Hom.: 6848

Bravo AF: 0.773

Asia WGS AF: 0.836 AC: 2907 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	2.3
DANN	Benign	0.85

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: rs2320615; hg19: chr4-164069949;