rs7415343

Variant names:

• chr1-100611767-T-C
• rs7415343
• ENST00000773974.1:n.164+8776A>G

Variant summary

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

The ENST00000773974.1(LINC01349):​n.164+8776A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 150,896 control chromosomes in the GnomAD database, including 37,970 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 0.69 (37970 hom., cov: 31)
• Consequence: LINC01349 ENST00000773974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 6 publications found

Genes affected

LINC01349 (HGNC:50568): (long intergenic non-protein coding RNA 1349)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773974.1. 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
	LINC01349	ENST00000773974.1		n.164+8776A>G		intron	N/A
	LINC01349	ENST00000773975.1		n.124+33403A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.688 AC: 103672 AN: 150784 Hom.: 37953 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.687 AC: 103728 AN: 150896 Hom.: 37970 Cov.: 31 AF XY: 0.688 AC XY: 50803 AN XY: 73818

African (AFR) AF: 0.397 AC: 16041 AN: 40356

American (AMR) AF: 0.756 AC: 11529 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2588 AN: 3470

East Asian (EAS) AF: 0.856 AC: 4428 AN: 5172

South Asian (SAS) AF: 0.808 AC: 3890 AN: 4812

European-Finnish (FIN) AF: 0.737 AC: 7780 AN: 10558

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55134 AN: 67972

Other (OTH) AF: 0.681 AC: 1433 AN: 2104

Alfa AF: 0.766 Hom.: 117979

Bravo AF: 0.670

Asia WGS AF: 0.795 AC: 2763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.23

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: rs7415343;

hg19: chr1-101077323;