rs35691538

Positions:

• chr8-125701794-G-A

Variant summary

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

The ENST00000651999.1(LINC02964):​n.211+21750G>A 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 0.0838 in 151,972 control chromosomes in the GnomAD database, including 1,161 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 0.084 (1161 hom., cov: 32)
• Consequence: LINC02964 ENST00000651999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

Genes affected

LINC02964 (HGNC:53487): (long intergenic non-protein coding RNA 2964)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02964	ENST00000651999.1	n.211+21750G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0837 AC: 12704 AN: 151854 Hom.: 1157 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0604

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.00869

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0262

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0838 AC: 12729 AN: 151972 Hom.: 1161 Cov.: 32 AF XY: 0.0805 AC XY: 5979 AN XY: 74306

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.0504

Gnomad4 ASJ AF: 0.0604

Gnomad4 EAS AF: 0.0217

Gnomad4 SAS AF: 0.0404

Gnomad4 FIN AF: 0.00869

Gnomad4 NFE AF: 0.0262

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0609 Hom.: 92

Bravo AF: 0.0943

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.48
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35691538; hg19: chr8-126714038;