8-122498498-G-C

Variant names:

• chr8-122498498-G-C
• rs10808523
• ENST00000664854.1:n.472-13170C>G

Variant summary

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

The NR_131202.1(SMILR):​n.163+69079C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,042 control chromosomes in the GnomAD database, including 26,487 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 0.57 (26487 hom., cov: 32)
• Consequence: SMILR NR_131202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 1 publications found

Genes affected

LINC01151 (HGNC:49471): (long intergenic non-protein coding RNA 1151)

SMILR (HGNC:51825): (smooth muscle induced lncRNA, enhancer of proliferation)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_131202.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMILR	NR_131202.1		n.163+69079C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01151	ENST00000664854.1		n.472-13170C>G		intron	N/A
	LINC01151	ENST00000702334.1		n.210-13170C>G		intron	N/A
	LINC01151	ENST00000718400.1		n.211-11032C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87024 AN: 151924 Hom.: 26445 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.573 AC: 87124 AN: 152042 Hom.: 26487 Cov.: 32 AF XY: 0.566 AC XY: 42071 AN XY: 74310

African (AFR) AF: 0.797 AC: 33085 AN: 41490

American (AMR) AF: 0.519 AC: 7929 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2503 AN: 5160

South Asian (SAS) AF: 0.513 AC: 2469 AN: 4810

European-Finnish (FIN) AF: 0.389 AC: 4108 AN: 10560

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33204 AN: 67960

Other (OTH) AF: 0.569 AC: 1203 AN: 2114

Alfa AF: 0.276 Hom.: 487

Bravo AF: 0.589

Asia WGS AF: 0.518 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.62
DANN	Benign	0.40
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10808523; hg19: chr8-123510737;