rs530157

Variant names:

• chr1-185564770-G-A
• rs530157
• ENST00000608417.6:n.167-1442C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-185564770-G-A
• chr1-185564770-G-C

Variant summary

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

The ENST00000608417.6(LINC01350):​n.167-1442C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,058 control chromosomes in the GnomAD database, including 15,434 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 0.44 (15434 hom., cov: 33)
• Consequence: LINC01350 ENST00000608417.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 1 publications found

Genes affected

LINC01350 (HGNC:50575): (long intergenic non-protein coding RNA 1350)

LOC107985239 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608417.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01350	NR_110793.1		n.147-1442C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01350	ENST00000608417.6	TSL:1	n.167-1442C>T		intron	N/A
	LINC01350	ENST00000439633.7	TSL:5	n.406+704C>T		intron	N/A
	LINC01350	ENST00000609066.6	TSL:2	n.402+704C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66246 AN: 151938 Hom.: 15419 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.436 AC: 66298 AN: 152058 Hom.: 15434 Cov.: 33 AF XY: 0.438 AC XY: 32551 AN XY: 74314

African (AFR) AF: 0.583 AC: 24174 AN: 41450

American (AMR) AF: 0.315 AC: 4810 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3470

East Asian (EAS) AF: 0.150 AC: 777 AN: 5176

South Asian (SAS) AF: 0.418 AC: 2017 AN: 4824

European-Finnish (FIN) AF: 0.501 AC: 5298 AN: 10582

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.395 AC: 26824 AN: 67970

Other (OTH) AF: 0.411 AC: 868 AN: 2110

Alfa AF: 0.291 Hom.: 763

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.062
DANN	Benign	0.56
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs530157;

hg19: chr1-185533902;