rs7244215

Variant names:

• chr18-70376080-G-A
• rs7244215
• ENST00000783305.1:n.319-22808G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-70376080-G-A
• chr18-70376080-G-T

Variant summary

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

The ENST00000783305.1(LINC01909):​n.319-22808G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,722 control chromosomes in the GnomAD database, including 5,142 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 0.26 (5142 hom., cov: 31)
• Consequence: LINC01909 ENST00000783305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 4 publications found

Genes affected

LINC01909 (HGNC:52728): (long intergenic non-protein coding RNA 1909)

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 = 0.297 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
LINC01909	ENST00000783305.1	n.319-22808G>A		intron_variant	Intron 3 of 3
LINC01909	ENST00000783306.1	n.50-14982G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38779 AN: 151604 Hom.: 5131 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.256 AC: 38824 AN: 151722 Hom.: 5142 Cov.: 31 AF XY: 0.247 AC XY: 18303 AN XY: 74150

African (AFR) AF: 0.229 AC: 9459 AN: 41374

American (AMR) AF: 0.221 AC: 3370 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3468

East Asian (EAS) AF: 0.135 AC: 690 AN: 5120

South Asian (SAS) AF: 0.216 AC: 1035 AN: 4788

European-Finnish (FIN) AF: 0.185 AC: 1961 AN: 10580

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.300 AC: 20383 AN: 67856

Other (OTH) AF: 0.276 AC: 581 AN: 2106

Alfa AF: 0.280 Hom.: 19231

Bravo AF: 0.257

Asia WGS AF: 0.170 AC: 593 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	2.3
DANN	Benign	0.36
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs7244215; hg19: chr18-68043316;