rs11576210

Variant names:

• chr1-99526816-G-T
• rs11576210
• ENST00000438829.2:n.23+7177C>A

Variant summary

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

The ENST00000438829.2(LINC01708):​n.23+7177C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,734 control chromosomes in the GnomAD database, including 8,411 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 0.30 (8411 hom., cov: 30)
• Consequence: LINC01708 ENST00000438829.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

Genes affected

LINC01708 (HGNC:52496): (long intergenic non-protein coding RNA 1708)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01708	ENST00000438829.2	n.23+7177C>A		intron_variant	Intron 1 of 3	5
LINC01708	ENST00000635551.1	n.164-39012C>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46102 AN: 151616 Hom.: 8415 Cov.: 30

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.304 AC: 46094 AN: 151734 Hom.: 8411 Cov.: 30 AF XY: 0.298 AC XY: 22054 AN XY: 74128

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.0662

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.344

Alfa AF: 0.338 Hom.: 1586

Bravo AF: 0.295

Asia WGS AF: 0.166 AC: 583 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
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: rs11576210; hg19: chr1-99992372;