chr10-37323908-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 41 gene

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+8107G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290801	ENST00000426471.6	TSL:2	n.314+8107G>T		intron	N/A
	ENSG00000290801	ENST00000435629.5	TSL:3	n.203+8107G>T		intron	N/A
	ENSG00000290801	ENST00000606476.1	TSL:5	n.157+8107G>T		intron	N/A

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

African (AFR) AF: 0.00501 AC: 208 AN: 41548

American (AMR) AF: 0.0105 AC: 161 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4814

European-Finnish (FIN) AF: 0.0179 AC: 190 AN: 10604

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0291 AC: 1978 AN: 68020

Other (OTH) AF: 0.0203 AC: 43 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.51
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12359948; hg19: chr10-37612836;