ENST00000528090.5:n.328-12208A>G

Variant names:

• chr8-124929255-A-G
• rs11776042
• ENST00000528090.5:n.328-12208A>G

Variant summary

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

The ENST00000528090.5(LINC00964):​n.328-12208A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,984 control chromosomes in the GnomAD database, including 22,489 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 0.53 (22489 hom., cov: 31)
• Consequence: LINC00964 ENST00000528090.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 11 publications found

Genes affected

LINC00964 (HGNC:27226): (long intergenic non-protein coding RNA 964)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00964	ENST00000528090.5	n.328-12208A>G		intron_variant	Intron 3 of 5	4
LINC00964	ENST00000654805.2	n.475-12208A>G		intron_variant	Intron 3 of 5
LINC00964	ENST00000655637.2	n.495-12208A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80095 AN: 151866 Hom.: 22482 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.527 AC: 80128 AN: 151984 Hom.: 22489 Cov.: 31 AF XY: 0.527 AC XY: 39143 AN XY: 74288

African (AFR) AF: 0.349 AC: 14481 AN: 41434

American (AMR) AF: 0.447 AC: 6828 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2270 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2030 AN: 5158

South Asian (SAS) AF: 0.614 AC: 2958 AN: 4818

European-Finnish (FIN) AF: 0.644 AC: 6799 AN: 10562

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42884 AN: 67942

Other (OTH) AF: 0.536 AC: 1131 AN: 2112

Alfa AF: 0.575 Hom.: 5754

Bravo AF: 0.504

Asia WGS AF: 0.519 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.37
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11776042; hg19: chr8-125941497;