1-99526816-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438829.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01708	ENST00000438829.2	TSL:5	n.23+7177C>A		intron	N/A
	LINC01708	ENST00000635551.1	TSL:5	n.164-39012C>A		intron	N/A
	LINC01708	ENST00000827173.1		n.37+7177C>A		intron	N/A

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

African (AFR) AF: 0.125 AC: 5168 AN: 41414

American (AMR) AF: 0.330 AC: 5018 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1311 AN: 3456

East Asian (EAS) AF: 0.0662 AC: 343 AN: 5180

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3614 AN: 10512

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28187 AN: 67836

Other (OTH) AF: 0.344 AC: 722 AN: 2098

Alfa AF: 0.355 Hom.: 17419

Bravo AF: 0.295

Asia WGS AF: 0.166 AC: 583 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.51
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs11576210; hg19: chr1-99992372;