rs1926123

chr10-37321867-G-T

Variant summary

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

The NR_104061.1(LINC00993):n.313+6066G>T 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 0.0894 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: LINC00993 NR_104061.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00993	NR_104061.1	n.313+6066G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000426471.6	n.314+6066G>T		intron_variant, non_coding_transcript_variant		2
	ENST00000435629.5	n.203+6066G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000606476.1	n.157+6066G>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.0606

Gnomad4 EAS AF: 0.0984

Gnomad4 SAS AF: 0.0728

Gnomad4 FIN AF: 0.0458

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0950

Alfa AF: 0.0750 Hom.: 212

Bravo AF: 0.0947

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	2.5
Dann	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1926123; hg19: chr10-37610795;