chr3-176421737-T-C

Variant names:

• chr3-176421737-T-C
• rs301193
• ENST00000652470.1:n.350-741A>G

Variant summary

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

The ENST00000652470.1(LINC01208):​n.350-741A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,182 control chromosomes in the GnomAD database, including 1,203 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 0.12 (1203 hom., cov: 32)
• Consequence: LINC01208 ENST00000652470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 3 publications found

Genes affected

LINC01208 (HGNC:49639): (long intergenic non-protein coding RNA 1208)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652470.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01208	ENST00000652470.1		n.350-741A>G		intron	N/A
	LINC01208	ENST00000785771.1		n.70-741A>G		intron	N/A
	LINC01208	ENST00000785773.1		n.122-741A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17589 AN: 152064 Hom.: 1200 Cov.: 32

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0984

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0577

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.116 AC: 17603 AN: 152182 Hom.: 1203 Cov.: 32 AF XY: 0.110 AC XY: 8217 AN XY: 74386

African (AFR) AF: 0.0698 AC: 2900 AN: 41564

American (AMR) AF: 0.0983 AC: 1502 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0578 AC: 279 AN: 4830

European-Finnish (FIN) AF: 0.128 AC: 1355 AN: 10596

Middle Eastern (MID) AF: 0.0586 AC: 17 AN: 290

European-Non Finnish (NFE) AF: 0.159 AC: 10813 AN: 67946

Other (OTH) AF: 0.126 AC: 266 AN: 2108

Alfa AF: 0.144 Hom.: 835

Bravo AF: 0.114

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs301193; hg19: chr3-176139525;