rs1048828

chr10-118365003-T-Achr10-118365003-T-G

Variant summary

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

The ENST00000668223.1(LINC00867):n.469+7155T>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 0.427 in 152,094 control chromosomes in the GnomAD database, including 15,688 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 0.43 (15686 hom., cov: 32)
  • Exomes 𝑓: 0.43 (2 hom.)
• Consequence: LINC00867 ENST00000668223.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

LINC00867 (HGNC:45265): (long intergenic non-protein coding RNA 867)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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
LINC00867	ENST00000668223.1	n.469+7155T>A		intron_variant, non_coding_transcript_variant
LINC00867	ENST00000415417.6	n.720T>A		non_coding_transcript_exon_variant	4/4	3
LINC00867	ENST00000453236.2	n.921T>A		non_coding_transcript_exon_variant	3/3	3
LINC00867	ENST00000657224.1	n.707T>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65020 AN: 151960 Hom.: 15697 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.423

GnomAD4 exome AF: 0.429 AC: 6 AN: 14 Hom.: 2 Cov.: 0 AF XY: 0.417 AC XY: 5 AN XY: 12

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.427 AC: 65010 AN: 152080 Hom.: 15686 Cov.: 32 AF XY: 0.433 AC XY: 32213 AN XY: 74330

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.418

Alfa AF: 0.483 Hom.: 2353

Bravo AF: 0.392

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	11
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1048828; hg19: chr10-120124515;