8-122498498-G-C

Position:

• chr8-122498498-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01151 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMILR	NR_131202.1	n.163+69079C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01151	ENST00000664854.1	n.472-13170C>G		intron_variant
LINC01151	ENST00000702334.1	n.210-13170C>G		intron_variant

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

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.569

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10808523; hg19: chr8-123510737;