rs6104690

Positions:

• chr20-11007451-G-A
• chr20-11007451-G-C
• chr20-11007451-G-T

Variant summary

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

The ENST00000659767.1(LINC02871):​n.625+8753G>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 0.559 in 151,948 control chromosomes in the GnomAD database, including 23,860 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 0.56 (23860 hom., cov: 32)
• Consequence: LINC02871 ENST00000659767.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

LINC02871 (HGNC:16180): (long intergenic non-protein coding RNA 2871)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 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
LINC02871	ENST00000659767.1	n.625+8753G>A		intron_variant, non_coding_transcript_variant
LINC02871	ENST00000662726.1	n.634+6170G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84839 AN: 151830 Hom.: 23848 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.559 AC: 84888 AN: 151948 Hom.: 23860 Cov.: 32 AF XY: 0.555 AC XY: 41198 AN XY: 74262

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.576

Alfa AF: 0.553 Hom.: 46159

Bravo AF: 0.563

Asia WGS AF: 0.517 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6104690; hg19: chr20-10988099;