rs10170218

Variant names:

• chr2-187949717-A-C
• rs10170218
• ENST00000434418.2:n.496+85879T>G

Variant summary

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

The ENST00000434418.2(LINC01090):​n.496+85879T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,058 control chromosomes in the GnomAD database, including 5,116 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 0.25 (5116 hom., cov: 32)
• Consequence: LINC01090 ENST00000434418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 7 publications found

Genes affected

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 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
LINC01090	ENST00000434418.2	n.496+85879T>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38549 AN: 151940 Hom.: 5108 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.254 AC: 38574 AN: 152058 Hom.: 5116 Cov.: 32 AF XY: 0.254 AC XY: 18915 AN XY: 74334

African (AFR) AF: 0.192 AC: 7957 AN: 41452

American (AMR) AF: 0.235 AC: 3595 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2252 AN: 5166

South Asian (SAS) AF: 0.267 AC: 1285 AN: 4812

European-Finnish (FIN) AF: 0.313 AC: 3306 AN: 10564

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18528 AN: 67998

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.266 Hom.: 23555

Bravo AF: 0.249

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10170218; hg19: chr2-188814444;