rs11776042

Positions:

• chr8-124929255-A-G

Variant summary

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

The ENST00000657463.1(LINC00964):​n.270-12208A>G variant causes a intron, non coding transcript 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 ENST00000657463.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00964	ENST00000657463.1	n.270-12208A>G		intron_variant, non_coding_transcript_variant

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;