rs12547950

Variant names:

• chr8-122603858-G-A
• rs12547950
• ENST00000664854.1:n.471+66502C>T

Variant summary

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

The ENST00000664854.1(LINC01151):​n.471+66502C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,162 control chromosomes in the GnomAD database, including 9,902 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 (9902 hom., cov: 33)
• Consequence: LINC01151 ENST00000664854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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
LINC01151	ENST00000664854.1	n.471+66502C>T		intron_variant	Intron 3 of 3
LINC01151	ENST00000667010.1	n.597-41147C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39319 AN: 152044 Hom.: 9858 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0580

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.0949

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.259 AC: 39411 AN: 152162 Hom.: 9902 Cov.: 33 AF XY: 0.252 AC XY: 18745 AN XY: 74392

African (AFR) AF: 0.664 AC: 27534 AN: 41474

American (AMR) AF: 0.163 AC: 2490 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3466

East Asian (EAS) AF: 0.0852 AC: 442 AN: 5188

South Asian (SAS) AF: 0.192 AC: 926 AN: 4822

European-Finnish (FIN) AF: 0.0580 AC: 615 AN: 10600

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.0949 AC: 6451 AN: 68002

Other (OTH) AF: 0.222 AC: 469 AN: 2114

Alfa AF: 0.149 Hom.: 5642

Bravo AF: 0.285

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.54
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs12547950; hg19: chr8-123616097;