chr10-37276059-T-C

Variant names:

• chr10-37276059-T-C
• rs1200826
• ENST00000420453.1:n.350+11422T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420453.1(LINC00993):​n.350+11422T>C variant causes a intron change. The variant allele was found at a frequency of 0.548 in 152,078 control chromosomes in the GnomAD database, including 23,298 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 0.55 (23298 hom., cov: 32)
• Consequence: LINC00993 ENST00000420453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.723 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
LINC00993	ENST00000420453.1	n.350+11422T>C		intron_variant	Intron 4 of 5	6

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83203 AN: 151958 Hom.: 23254 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.548 AC: 83302 AN: 152078 Hom.: 23298 Cov.: 32 AF XY: 0.553 AC XY: 41144 AN XY: 74336

African (AFR) AF: 0.624 AC: 25875 AN: 41492

American (AMR) AF: 0.535 AC: 8174 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1715 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3701 AN: 5156

South Asian (SAS) AF: 0.743 AC: 3579 AN: 4816

European-Finnish (FIN) AF: 0.545 AC: 5763 AN: 10584

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.482 AC: 32753 AN: 67964

Other (OTH) AF: 0.534 AC: 1125 AN: 2108

Alfa AF: 0.516 Hom.: 15126

Bravo AF: 0.544

Asia WGS AF: 0.716 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1200826; hg19: chr10-37564987;