rs638882

Positions:

• chr11-115893327-C-T

Variant summary

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

The XR_001748394.3(LINC02698):​n.469-7409C>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 0.462 in 151,994 control chromosomes in the GnomAD database, including 16,303 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 0.46 (16303 hom., cov: 32)
• Consequence: LINC02698 XR_001748394.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

Genes affected

LINC02698 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02698	XR_001748394.3	n.469-7409C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70078 AN: 151876 Hom.: 16280 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.462 AC: 70146 AN: 151994 Hom.: 16303 Cov.: 32 AF XY: 0.461 AC XY: 34254 AN XY: 74290

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.470

Alfa AF: 0.442 Hom.: 17483

Bravo AF: 0.480

Asia WGS AF: 0.433 AC: 1505 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	0.0080
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs638882; hg19: chr11-115764045;