rs11156473

Variant names:

• chr10-131772532-G-A
• rs11156473
• ENST00000341866.3:n.3250C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-131772532-G-A
• chr10-131772532-G-T

Variant summary

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

The ENST00000341866.3(LINC01164):​n.3250C>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 0.13 in 152,352 control chromosomes in the GnomAD database, including 1,875 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 0.13 (1873 hom., cov: 33)
  • Exomes 𝑓: 0.12 (2 hom.)
• Consequence: LINC01164 ENST00000341866.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 1 publications found

Genes affected

LINC01164 (HGNC:49533): (long intergenic non-protein coding RNA 1164)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000341866.3. 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
	LINC01164	NR_038365.1		n.3250C>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01164	ENST00000341866.3	TSL:2	n.3250C>T		non_coding_transcript_exon	Exon 5 of 5
	LINC01164	ENST00000655798.1		n.2650C>T		non_coding_transcript_exon	Exon 6 of 6
	LINC01164	ENST00000667493.1		n.3141C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19760 AN: 152052 Hom.: 1873 Cov.: 33

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.121 AC: 22 AN: 182 Hom.: 2 Cov.: 0 AF XY: 0.132 AC XY: 19 AN XY: 144

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 6

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.313 AC: 5 AN: 16

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0956 AC: 13 AN: 136

Other (OTH) AF: 0.250 AC: 3 AN: 12

GnomAD4 genome AF: 0.130 AC: 19753 AN: 152170 Hom.: 1873 Cov.: 33 AF XY: 0.135 AC XY: 10010 AN XY: 74368

African (AFR) AF: 0.0309 AC: 1282 AN: 41550

American (AMR) AF: 0.119 AC: 1814 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3472

East Asian (EAS) AF: 0.448 AC: 2297 AN: 5126

South Asian (SAS) AF: 0.356 AC: 1713 AN: 4814

European-Finnish (FIN) AF: 0.145 AC: 1533 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10233 AN: 67996

Other (OTH) AF: 0.166 AC: 350 AN: 2112

Alfa AF: 0.0917 Hom.: 213

Bravo AF: 0.121

Asia WGS AF: 0.365 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11156473; hg19: chr10-133604868;