rs1099399

Variant names:

• chr12-127868130-C-A
• rs1099399
• ENST00000741352.1:n.317-6274G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-127868130-C-A
• chr12-127868130-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000741352.1(LINC00508):​n.317-6274G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0303 in 152,044 control chromosomes in the GnomAD database, including 169 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 0.030 (169 hom., cov: 31)
• Consequence: LINC00508 ENST00000741352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 2 publications found

Genes affected

LINC00508 (HGNC:43559): (long intergenic non-protein coding RNA 508)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.091 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
LINC00508	ENST00000741352.1	n.317-6274G>T		intron_variant	Intron 3 of 3
LINC00508	ENST00000741353.1	n.406-6274G>T		intron_variant	Intron 4 of 4
LINC00508	ENST00000741354.1	n.435-6274G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0302 AC: 4581 AN: 151928 Hom.: 169 Cov.: 31

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00252

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.00537

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00475

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0303 AC: 4604 AN: 152044 Hom.: 169 Cov.: 31 AF XY: 0.0297 AC XY: 2211 AN XY: 74340

African (AFR) AF: 0.0934 AC: 3871 AN: 41424

American (AMR) AF: 0.0117 AC: 179 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5156

South Asian (SAS) AF: 0.0156 AC: 75 AN: 4804

European-Finnish (FIN) AF: 0.00537 AC: 57 AN: 10608

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

European-Non Finnish (NFE) AF: 0.00475 AC: 323 AN: 68006

Other (OTH) AF: 0.0209 AC: 44 AN: 2110

Alfa AF: 0.000255 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.49
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs1099399; hg19: chr12-128352675;