rs11783570

chr8-66192136-T-C

Variant summary

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

The NR_039979.1(LINC00967):n.23T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 152,444 control chromosomes in the GnomAD database, including 205 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 0.043 (205 hom., cov: 32)
  • Exomes 𝑓: 0.051 (0 hom.)
• Consequence: LINC00967 NR_039979.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

Genes affected

LINC00967 (HGNC:48725): (long intergenic non-protein coding RNA 967)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00967	NR_039979.1	n.23T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00967	ENST00000518035.5	n.26T>C		non_coding_transcript_exon_variant	1/3	2
LINC00967	ENST00000517725.1	n.22T>C		non_coding_transcript_exon_variant	1/3	2
LINC00967	ENST00000518412.1	n.44T>C		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes AF: 0.0435 AC: 6616 AN: 152208 Hom.: 205 Cov.: 32

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0478

GnomAD4 exome AF: 0.0508 AC: 6 AN: 118 Hom.: 0 Cov.: 0 AF XY: 0.0581 AC XY: 5 AN XY: 86

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0568

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0434 AC: 6613 AN: 152326 Hom.: 205 Cov.: 32 AF XY: 0.0438 AC XY: 3261 AN XY: 74480

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0337

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0734

Gnomad4 NFE AF: 0.0617

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0528 Hom.: 57

Bravo AF: 0.0386

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.16
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11783570; hg19: chr8-67104371;