rs2146204

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00970 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00970	NR_104091.1	n.322-149T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00970	ENST00000366408.3	n.322-149T>G		intron_variant		1
ENSG00000285622	ENST00000650631.1	n.413+116082T>G		intron_variant

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

Gnomad4 AFR AF: 0.0862

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0714

Gnomad4 SAS AF: 0.0921

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.116

Alfa AF: 0.139 Hom.: 2143

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2146204; hg19: chr1-168874099;