rs11776042

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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	ENST00000654805.1	n.423-12208A>G		intron_variant	Intron 3 of 5
LINC00964	ENST00000655637.1	n.474-12208A>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

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.536

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11776042; hg19: chr8-125941497;