10-37270652-A-G

Variant names:

• chr10-37270652-A-G
• rs1200821
• ENST00000420453.1:n.350+6015A>G

Variant summary

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

The ENST00000420453.1(LINC00993):​n.350+6015A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420453.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00993	ENST00000420453.1	TSL:6	n.350+6015A>G		intron	N/A

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

African (AFR) AF: 0.478 AC: 19780 AN: 41408

American (AMR) AF: 0.507 AC: 7739 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3466

East Asian (EAS) AF: 0.666 AC: 3429 AN: 5152

South Asian (SAS) AF: 0.722 AC: 3478 AN: 4816

European-Finnish (FIN) AF: 0.543 AC: 5710 AN: 10518

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32096 AN: 67920

Other (OTH) AF: 0.483 AC: 1021 AN: 2112

Alfa AF: 0.487 Hom.: 27965

Bravo AF: 0.488

Asia WGS AF: 0.669 AC: 2326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.44
PhyloP100		2.2
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: rs1200821; hg19: chr10-37559580;