rs1419112

Variant names:

• chr10-89939914-A-G
• rs1419112
• ENST00000428485.1:n.577+15961T>C

Variant summary

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

The ENST00000428485.1(LINC01375):​n.577+15961T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,256 control chromosomes in the GnomAD database, including 624 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 0.083 (624 hom., cov: 32)
• Consequence: LINC01375 ENST00000428485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 2 publications found

Genes affected

LINC01375 (HGNC:50632): (long intergenic non-protein coding RNA 1375)

LINC00865 (HGNC:45170): (long intergenic non-protein coding RNA 865)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428485.1. 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
	LINC01375	NR_110655.1		n.577+15961T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01375	ENST00000428485.1	TSL:2	n.577+15961T>C		intron	N/A
	LINC00865	ENST00000664430.1		n.548+25144A>G		intron	N/A
	LINC00865	ENST00000715760.1		n.740+25144A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0831 AC: 12646 AN: 152138 Hom.: 624 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.0832 AC: 12661 AN: 152256 Hom.: 624 Cov.: 32 AF XY: 0.0846 AC XY: 6300 AN XY: 74444

African (AFR) AF: 0.0965 AC: 4006 AN: 41526

American (AMR) AF: 0.0714 AC: 1093 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3468

East Asian (EAS) AF: 0.138 AC: 713 AN: 5174

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4820

European-Finnish (FIN) AF: 0.0365 AC: 387 AN: 10614

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4664 AN: 68034

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.0758 Hom.: 323

Bravo AF: 0.0830

Asia WGS AF: 0.190 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.66
PhyloP100		1.3

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: rs1419112;

hg19: chr10-91699671;