11-129612280-A-G

Variant names:

• chr11-129612280-A-G
• rs10750417
• ENST00000631195.1:n.818T>C

Variant summary

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

The ENST00000631195.1(LINC01395):​n.818T>C 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 0.701 in 151,992 control chromosomes in the GnomAD database, including 37,458 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 0.70 (37455 hom., cov: 31)
  • Exomes 𝑓: 0.67 (3 hom.)
• Consequence: LINC01395 ENST00000631195.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 5 publications found

Genes affected

LINC01395 (HGNC:50674): (long intergenic non-protein coding RNA 1395)

ENSG00000281386 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631195.1. 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
	LINC01395	NR_120582.1		n.818T>C		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01395	ENST00000631195.1	TSL:1	n.818T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000281386	ENST00000626400.2	TSL:4	n.699A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106431 AN: 151862 Hom.: 37445 Cov.: 31

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.716

GnomAD4 exome AF: 0.667 AC: 8 AN: 12 Hom.: 3 Cov.: 0 AF XY: 0.800 AC XY: 8 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

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: 0.625 AC: 5 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.701 AC: 106483 AN: 151980 Hom.: 37455 Cov.: 31 AF XY: 0.702 AC XY: 52137 AN XY: 74290

African (AFR) AF: 0.643 AC: 26635 AN: 41436

American (AMR) AF: 0.745 AC: 11380 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2407 AN: 3472

East Asian (EAS) AF: 0.778 AC: 4017 AN: 5162

South Asian (SAS) AF: 0.805 AC: 3879 AN: 4820

European-Finnish (FIN) AF: 0.663 AC: 6989 AN: 10538

Middle Eastern (MID) AF: 0.788 AC: 230 AN: 292

European-Non Finnish (NFE) AF: 0.719 AC: 48893 AN: 67968

Other (OTH) AF: 0.715 AC: 1508 AN: 2110

Alfa AF: 0.720 Hom.: 65758

Bravo AF: 0.703

Asia WGS AF: 0.788 AC: 2739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.0
DANN	Benign	0.51
PhyloP100		1.0

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: rs10750417;

hg19: chr11-129482175;