chr10-65002965-G-A

Position:

• chr10-65002965-G-A

Variant summary

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

The ENST00000655566.1(LINC02671):​n.89-2715C>T 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 0.316 in 151,858 control chromosomes in the GnomAD database, including 7,842 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 0.32 (7842 hom., cov: 33)
• Consequence: LINC02671 ENST00000655566.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

Genes affected

LINC02671 (HGNC:54158): (long intergenic non-protein coding RNA 2671)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 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
LINC02671	ENST00000655566.1	n.89-2715C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47984 AN: 151740 Hom.: 7840 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.316 AC: 48008 AN: 151858 Hom.: 7842 Cov.: 33 AF XY: 0.319 AC XY: 23654 AN XY: 74214

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.319

Alfa AF: 0.301 Hom.: 1136

Bravo AF: 0.312

Asia WGS AF: 0.267 AC: 924 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	10
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7904001; hg19: chr10-66762723;