rs7229302

Variant names:

• chr18-11508905-T-G
• rs7229302
• ENST00000661687.1:n.215-4292T>G

Variant summary

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

The ENST00000661687.1(LINC01255):​n.215-4292T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,736 control chromosomes in the GnomAD database, including 12,836 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 0.40 (12836 hom., cov: 33)
• Consequence: LINC01255 ENST00000661687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• Publications: 3 publications found

Genes affected

LINC01255 (HGNC:49871): (long intergenic non-protein coding RNA 1255)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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
LINC01255	ENST00000661687.1	n.215-4292T>G		intron_variant	Intron 1 of 3
LINC01255	ENST00000663721.1	n.153-9940T>G		intron_variant	Intron 1 of 2
LINC01255	ENST00000664813.1	n.175-5231T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60073 AN: 151618 Hom.: 12795 Cov.: 33

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.397 AC: 60167 AN: 151736 Hom.: 12836 Cov.: 33 AF XY: 0.402 AC XY: 29802 AN XY: 74148

African (AFR) AF: 0.536 AC: 22159 AN: 41348

American (AMR) AF: 0.429 AC: 6542 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3464

East Asian (EAS) AF: 0.584 AC: 3017 AN: 5162

South Asian (SAS) AF: 0.394 AC: 1893 AN: 4810

European-Finnish (FIN) AF: 0.370 AC: 3898 AN: 10524

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20197 AN: 67866

Other (OTH) AF: 0.391 AC: 824 AN: 2108

Alfa AF: 0.371 Hom.: 3190

Bravo AF: 0.407

Asia WGS AF: 0.508 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.56
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs7229302; hg19: chr18-11508904;