chr10-128306603-C-T

Variant names:

• chr10-128306603-C-T
• rs7914524
• ENST00000630252.1:n.905C>T

Variant summary

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

The ENST00000630252.1(LINC01163):​n.905C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,974 control chromosomes in the GnomAD database, including 3,959 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 0.22 (3959 hom., cov: 31)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: LINC01163 ENST00000630252.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.263 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
	LINC01163	NR_120619.1		n.830C>T		non_coding_transcript_exon	Exon 3 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01163	ENST00000630252.1	TSL:2	n.905C>T		non_coding_transcript_exon	Exon 4 of 7

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34001 AN: 151850 Hom.: 3960 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.224 AC: 34015 AN: 151968 Hom.: 3959 Cov.: 31 AF XY: 0.228 AC XY: 16902 AN XY: 74274

African (AFR) AF: 0.254 AC: 10539 AN: 41414

American (AMR) AF: 0.270 AC: 4125 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3468

East Asian (EAS) AF: 0.209 AC: 1075 AN: 5146

South Asian (SAS) AF: 0.256 AC: 1234 AN: 4812

European-Finnish (FIN) AF: 0.253 AC: 2674 AN: 10560

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13043 AN: 67966

Other (OTH) AF: 0.206 AC: 434 AN: 2106

Alfa AF: 0.188 Hom.: 2322

Bravo AF: 0.228

Asia WGS AF: 0.232 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7914524; hg19: chr10-130104867;