rs2146204

Variant names:

• chr1-168904861-A-C
• rs2146204
• ENST00000366408.3:n.322-149T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-168904861-A-C
• chr1-168904861-A-T

Variant summary

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

The ENST00000366408.3(LINC00970):​n.322-149T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,228 control chromosomes in the GnomAD database, including 1,385 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 (1385 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00970 ENST00000366408.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 4 publications found

Genes affected

LINC00970 (HGNC:):

LINC00970 (HGNC:48730): (long intergenic non-protein coding RNA 970)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00970	NR_104091.1	n.322-149T>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00970	ENST00000366408.3	n.322-149T>G		intron_variant	Intron 4 of 4	1
LINC00970	ENST00000457405.2	n.473-68373T>G		intron_variant	Intron 5 of 7	3
LINC00970	ENST00000650631.1	n.413+116082T>G		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19386 AN: 152110 Hom.: 1382 Cov.: 32

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0712

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.128 AC: 19410 AN: 152228 Hom.: 1385 Cov.: 32 AF XY: 0.124 AC XY: 9254 AN XY: 74440

African (AFR) AF: 0.0862 AC: 3580 AN: 41540

American (AMR) AF: 0.102 AC: 1567 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3472

East Asian (EAS) AF: 0.0714 AC: 370 AN: 5184

South Asian (SAS) AF: 0.0921 AC: 444 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1621 AN: 10584

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10819 AN: 68010

Other (OTH) AF: 0.116 AC: 245 AN: 2116

Alfa AF: 0.138 Hom.: 2664

Bravo AF: 0.121

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.69
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2146204; hg19: chr1-168874099;