10-37323908-G-T

Variant names:

• chr10-37323908-G-T
• rs12359948
• ENST00000426471.6:n.314+8107G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000426471.6(ENSG00000290801):​n.314+8107G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 152,254 control chromosomes in the GnomAD database, including 41 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 0.019 (41 hom., cov: 32)
• Consequence: ENSG00000290801 ENST00000426471.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

Genes affected

ENSG00000290801 (HGNC:):

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=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0188 (2857/152254) while in subpopulation NFE AF= 0.0291 (1978/68020). AF 95% confidence interval is 0.028. There are 41 homozygotes in gnomad4. There are 1387 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 41 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00993	NR_104061.1	n.313+8107G>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290801	ENST00000426471.6	n.314+8107G>T		intron_variant	Intron 3 of 4	2
ENSG00000290801	ENST00000435629.5	n.203+8107G>T		intron_variant	Intron 3 of 4	3
ENSG00000290801	ENST00000606476.1	n.157+8107G>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2858 AN: 152136 Hom.: 41 Cov.: 32

Gnomad AFR AF: 0.00502

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0105

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0291

Gnomad OTH AF: 0.0205

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

GnomAD4 genome AF: 0.0188 AC: 2857 AN: 152254 Hom.: 41 Cov.: 32 AF XY: 0.0186 AC XY: 1387 AN XY: 74436

Gnomad4 AFR AF: 0.00501

Gnomad4 AMR AF: 0.0105

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0291

Gnomad4 OTH AF: 0.0203

Alfa AF: 0.0125 Hom.: 4

Bravo AF: 0.0179

Asia WGS AF: 0.00577 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12359948; hg19: chr10-37612836;