rs10494476

Variant names:

• chr1-169031256-G-A
• rs10494476
• ENST00000366408.3:n.209+24928C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-169031256-G-A
• chr1-169031256-G-C

Variant summary

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

The ENST00000366408.3(LINC00970):​n.209+24928C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,152 control chromosomes in the GnomAD database, including 1,464 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 (1464 hom., cov: 32)
• Consequence: LINC00970 ENST00000366408.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366408.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00970	NR_104091.1		n.209+24928C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00970	ENST00000366408.3	TSL:1	n.209+24928C>T		intron	N/A
	LINC00970	ENST00000457405.2	TSL:3	n.349-10190C>T		intron	N/A
	LINC00970	ENST00000650631.1		n.290-10190C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19067 AN: 152034 Hom.: 1465 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0881

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.0907

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.125 AC: 19086 AN: 152152 Hom.: 1464 Cov.: 32 AF XY: 0.127 AC XY: 9465 AN XY: 74372

African (AFR) AF: 0.196 AC: 8129 AN: 41488

American (AMR) AF: 0.173 AC: 2639 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0881 AC: 306 AN: 3472

East Asian (EAS) AF: 0.0496 AC: 257 AN: 5186

South Asian (SAS) AF: 0.0912 AC: 440 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1344 AN: 10576

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5610 AN: 68004

Other (OTH) AF: 0.103 AC: 218 AN: 2114

Alfa AF: 0.0928 Hom.: 3236

Bravo AF: 0.131

Asia WGS AF: 0.0750 AC: 263 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10494476; hg19: chr1-169000494;