ENST00000668811.1:n.1919G>A

Variant names:

• chr13-44243049-C-T
• rs10507528
• ENST00000668811.1:n.1919G>A

Variant summary

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

The ENST00000668811.1(LINC02938):​n.1919G>A 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 152,272 control chromosomes in the GnomAD database, including 357 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 (357 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02938 ENST00000668811.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

Genes affected

LINC02938 (HGNC:55952): (long intergenic non-protein coding RNA 2938)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02938	ENST00000668811.1	n.1919G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02938	ENST00000421190.2	n.58+86G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6594 AN: 152152 Hom.: 358 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0166

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.00640

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00631

Gnomad OTH AF: 0.0406

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 110 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 86

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0434 AC: 6603 AN: 152272 Hom.: 357 Cov.: 33 AF XY: 0.0437 AC XY: 3251 AN XY: 74472

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0165

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.0683

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.00640

Gnomad4 NFE AF: 0.00631

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0265 Hom.: 24

Bravo AF: 0.0467

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507528; hg19: chr13-44817185;