rs10507528

chr13-44243049-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02938	ENST00000668811.1	n.1919G>A		non_coding_transcript_exon_variant	3/3
LINC02938	ENST00000421190.2	n.58+86G>A		intron_variant, non_coding_transcript_variant		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;