rs9296102

Variant names:

• chr6-33902029-G-A
• rs9296102
• ENST00000451317.2:n.119+1556G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-33902029-G-A
• chr6-33902029-G-T

Variant summary

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

The ENST00000451317.2(ENSG00000233183):​n.119+1556G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,996 control chromosomes in the GnomAD database, including 13,329 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 0.41 (13329 hom., cov: 32)
• Consequence: ENSG00000233183 ENST00000451317.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 8 publications found

Genes affected

ENSG00000233183 (HGNC:):

LINC01016 (HGNC:48991): (long intergenic non-protein coding RNA 1016)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375026	NR_187840.1	n.262+8639G>A		intron_variant	Intron 1 of 2
LOC105375026	NR_187841.1	n.262+8639G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233183	ENST00000451317.2	n.119+1556G>A		intron_variant	Intron 1 of 3	2
ENSG00000233183	ENST00000526556.1	n.68+8639G>A		intron_variant	Intron 1 of 1	3
ENSG00000233183	ENST00000655159.1	n.2+1556G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61820 AN: 151878 Hom.: 13300 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.407 AC: 61898 AN: 151996 Hom.: 13329 Cov.: 32 AF XY: 0.405 AC XY: 30116 AN XY: 74306

African (AFR) AF: 0.553 AC: 22916 AN: 41424

American (AMR) AF: 0.385 AC: 5874 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2202 AN: 5168

South Asian (SAS) AF: 0.462 AC: 2223 AN: 4810

European-Finnish (FIN) AF: 0.333 AC: 3515 AN: 10558

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22731 AN: 67980

Other (OTH) AF: 0.409 AC: 864 AN: 2112

Alfa AF: 0.355 Hom.: 15401

Bravo AF: 0.416

Asia WGS AF: 0.446 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.47
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs9296102; hg19: chr6-33869806;