rs1200821

chr10-37270652-A-Gchr10-37270652-A-T

Variant summary

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

The ENST00000420453.1(LINC00993):n.350+6015A>G 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 0.497 in 151,848 control chromosomes in the GnomAD database, including 19,062 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 0.50 (19062 hom., cov: 31)
• Consequence: LINC00993 ENST00000420453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21

Genes affected

LINC00993 (HGNC:48948): (long intergenic non-protein coding RNA 993)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.702 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
LINC00993	ENST00000420453.1	n.350+6015A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75494 AN: 151730 Hom.: 19058 Cov.: 31

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.497 AC: 75519 AN: 151848 Hom.: 19062 Cov.: 31 AF XY: 0.504 AC XY: 37410 AN XY: 74210

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.483

Alfa AF: 0.483 Hom.: 13496

Bravo AF: 0.488

Asia WGS AF: 0.669 AC: 2326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.1
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1200821; hg19: chr10-37559580;