rs1926123

Variant names:

• chr10-37321867-G-T
• rs1926123
• ENST00000426471.6:n.314+6066G>T

Variant summary

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

The ENST00000426471.6(ENSG00000290801):​n.314+6066G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 152,062 control chromosomes in the GnomAD database, including 758 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 0.089 (758 hom., cov: 32)
• Consequence: ENSG00000290801 ENST00000426471.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 2 publications found

Genes affected

ENSG00000290801 (HGNC:):

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426471.6. 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
	LINC00993	NR_104061.1		n.313+6066G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290801	ENST00000426471.6	TSL:2	n.314+6066G>T		intron	N/A
	ENSG00000290801	ENST00000435629.5	TSL:3	n.203+6066G>T		intron	N/A
	ENSG00000290801	ENST00000606476.1	TSL:5	n.157+6066G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0890 AC: 13520 AN: 151944 Hom.: 732 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0606

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0694

Gnomad OTH AF: 0.0945

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

GnomAD4 genome AF: 0.0894 AC: 13601 AN: 152062 Hom.: 758 Cov.: 32 AF XY: 0.0881 AC XY: 6551 AN XY: 74326

African (AFR) AF: 0.146 AC: 6067 AN: 41460

American (AMR) AF: 0.0599 AC: 915 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0606 AC: 210 AN: 3468

East Asian (EAS) AF: 0.0984 AC: 508 AN: 5160

South Asian (SAS) AF: 0.0728 AC: 350 AN: 4806

European-Finnish (FIN) AF: 0.0458 AC: 485 AN: 10588

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0693 AC: 4715 AN: 67994

Other (OTH) AF: 0.0950 AC: 200 AN: 2106

Alfa AF: 0.0755 Hom.: 241

Bravo AF: 0.0947

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.5
DANN	Benign	0.14
PhyloP100		-1.2
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: rs1926123; hg19: chr10-37610795;