4-79164788-C-T

Variant names:

• chr4-79164788-C-T
• rs10518214
• ENST00000509088.7:n.635-31048C>T

Variant summary

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

The ENST00000509088.7(LINC01088):​n.635-31048C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 152,102 control chromosomes in the GnomAD database, including 39,641 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 0.69 (39641 hom., cov: 32)
• Consequence: LINC01088 ENST00000509088.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 2 publications found

Genes affected

LINC01088 (HGNC:49148): (long intergenic non-protein coding RNA 1088)

NAA11 (HGNC:28125): (N-alpha-acetyltransferase 11, NatA catalytic subunit) Enables peptide alpha-N-acetyltransferase activity. Involved in N-terminal protein amino acid acetylation. Located in several cellular components, including Golgi apparatus; centrosome; and nucleoplasm. Part of NatA complex. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509088.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01088	NR_038342.1		n.350-31048C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01088	ENST00000509088.7	TSL:1	n.635-31048C>T		intron	N/A
	LINC01088	ENST00000510667.5	TSL:3	n.296+78526C>T		intron	N/A
	LINC01088	ENST00000513153.5	TSL:3	n.276+78526C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104536 AN: 151986 Hom.: 39638 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.687 AC: 104560 AN: 152102 Hom.: 39641 Cov.: 32 AF XY: 0.699 AC XY: 51959 AN XY: 74372

African (AFR) AF: 0.340 AC: 14107 AN: 41432

American (AMR) AF: 0.759 AC: 11612 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2665 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5149 AN: 5168

South Asian (SAS) AF: 0.877 AC: 4232 AN: 4824

European-Finnish (FIN) AF: 0.879 AC: 9310 AN: 10586

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55068 AN: 68012

Other (OTH) AF: 0.705 AC: 1489 AN: 2112

Alfa AF: 0.768 Hom.: 143857

Bravo AF: 0.666

Asia WGS AF: 0.878 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.41
DANN	Benign	0.63
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10518214; hg19: chr4-80085942;