rs4560755

Variant names:

• chr8-126280511-G-A
• rs4560755
• ENST00000651482.1:n.198+12080C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-126280511-G-A
• chr8-126280511-G-T

Variant summary

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

The ENST00000651482.1(LINC00861):​n.198+12080C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,006 control chromosomes in the GnomAD database, including 4,726 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 (4726 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 1 publications found

Genes affected

LINC00861 (HGNC:45133): (long intergenic non-protein coding RNA 861)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 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
LINC00861	ENST00000651482.1	n.198+12080C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37237 AN: 151888 Hom.: 4724 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.245 AC: 37242 AN: 152006 Hom.: 4726 Cov.: 32 AF XY: 0.247 AC XY: 18321 AN XY: 74290

African (AFR) AF: 0.181 AC: 7510 AN: 41462

American (AMR) AF: 0.239 AC: 3654 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 796 AN: 3472

East Asian (EAS) AF: 0.300 AC: 1542 AN: 5144

South Asian (SAS) AF: 0.301 AC: 1449 AN: 4818

European-Finnish (FIN) AF: 0.275 AC: 2905 AN: 10548

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

European-Non Finnish (NFE) AF: 0.271 AC: 18430 AN: 67956

Other (OTH) AF: 0.249 AC: 525 AN: 2112

Alfa AF: 0.259 Hom.: 2812

Bravo AF: 0.235

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.48
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4560755; hg19: chr8-127292756;