chr10-128200108-T-C

Variant names:

• chr10-128200108-T-C
• rs1329189
• ENST00000626518.2:n.125+18952T>C

Variant summary

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

The ENST00000630252.1(LINC01163):​n.77+18896T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,086 control chromosomes in the GnomAD database, including 39,463 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 0.72 (39463 hom., cov: 32)
• Consequence: LINC01163 ENST00000630252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 6 publications found

Genes affected

LINC01163 (HGNC:49530): (long intergenic non-protein coding RNA 1163)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000630252.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01163	ENST00000626518.2	TSL:4	n.125+18952T>C		intron	N/A
	LINC01163	ENST00000630252.1	TSL:2	n.77+18896T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108870 AN: 151964 Hom.: 39389 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.717 AC: 109009 AN: 152086 Hom.: 39463 Cov.: 32 AF XY: 0.712 AC XY: 52888 AN XY: 74326

African (AFR) AF: 0.814 AC: 33791 AN: 41522

American (AMR) AF: 0.679 AC: 10377 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2933 AN: 5156

South Asian (SAS) AF: 0.541 AC: 2610 AN: 4820

European-Finnish (FIN) AF: 0.673 AC: 7102 AN: 10548

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47662 AN: 67982

Other (OTH) AF: 0.706 AC: 1490 AN: 2110

Alfa AF: 0.697 Hom.: 167080

Bravo AF: 0.723

Asia WGS AF: 0.600 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1329189; hg19: chr10-129998372;