rs485499

Variant names:

• chr3-160028076-T-C
• rs485499
• ENST00000471921.2:n.495+1190T>C

Variant summary

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

The ENST00000471921.2(LINC01100):​n.495+1190T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,074 control chromosomes in the GnomAD database, including 7,722 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 0.29 (7722 hom., cov: 32)
• Consequence: LINC01100 ENST00000471921.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 40 publications found

Genes affected

LINC01100 (HGNC:49224): (long intergenic non-protein coding RNA 1100)

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

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 = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01100	NR_104132.1	n.373+1190T>C		intron_variant	Intron 2 of 2
IL12A-AS1	NR_108088.1	n.518-2542A>G		intron_variant	Intron 3 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01100	ENST00000471921.2	n.495+1190T>C		intron_variant	Intron 4 of 4	5
IL12A-AS1	ENST00000497452.5	n.518-2542A>G		intron_variant	Intron 3 of 9	2
IL12A-AS1	ENST00000642756.1	n.366+10834A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44495 AN: 151956 Hom.: 7718 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.293 AC: 44501 AN: 152074 Hom.: 7722 Cov.: 32 AF XY: 0.286 AC XY: 21244 AN XY: 74314

African (AFR) AF: 0.121 AC: 5024 AN: 41522

American (AMR) AF: 0.256 AC: 3908 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1004 AN: 3468

East Asian (EAS) AF: 0.138 AC: 712 AN: 5170

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4810

European-Finnish (FIN) AF: 0.363 AC: 3832 AN: 10558

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28015 AN: 67968

Other (OTH) AF: 0.279 AC: 588 AN: 2106

Alfa AF: 0.367 Hom.: 37925

Bravo AF: 0.278

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs485499; hg19: chr3-159745863;