chr10-121179860-T-C

Variant names:

• chr10-121179860-T-C
• rs7085142
• ENST00000429809.1:n.273+888T>C

Variant summary

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

The ENST00000429809.1(LINC01153):​n.273+888T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,064 control chromosomes in the GnomAD database, including 22,930 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 0.53 (22930 hom., cov: 33)
• Consequence: LINC01153 ENST00000429809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 8 publications found

Genes affected

LINC01153 (HGNC:49495): (long intergenic non-protein coding RNA 1153)

ENSG00000296663 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902515	XR_007062317.1	n.167+5518A>G		intron_variant	Intron 1 of 1
LOC124902515	XR_007062318.1	n.158+5527A>G		intron_variant	Intron 1 of 1
LINC01153	XR_246197.3	n.436+888T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01153	ENST00000429809.1	n.273+888T>C		intron_variant	Intron 1 of 1	1
ENSG00000296663	ENST00000741064.1	n.93+5518A>G		intron_variant	Intron 1 of 1
ENSG00000296663	ENST00000741065.1	n.84+5527A>G		intron_variant	Intron 1 of 1
ENSG00000296663	ENST00000741066.1	n.75+5518A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80130 AN: 151944 Hom.: 22932 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.527 AC: 80157 AN: 152064 Hom.: 22930 Cov.: 33 AF XY: 0.527 AC XY: 39179 AN XY: 74336

African (AFR) AF: 0.304 AC: 12602 AN: 41494

American (AMR) AF: 0.502 AC: 7669 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2374 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2202 AN: 5168

South Asian (SAS) AF: 0.782 AC: 3773 AN: 4824

European-Finnish (FIN) AF: 0.624 AC: 6581 AN: 10552

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42889 AN: 67966

Other (OTH) AF: 0.554 AC: 1167 AN: 2108

Alfa AF: 0.600 Hom.: 96452

Bravo AF: 0.500

Asia WGS AF: 0.567 AC: 1964 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.84
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs7085142; hg19: chr10-122939374;