chr5-97691782-A-G

Variant names:

• chr5-97691782-A-G
• rs1560326
• ENST00000715761.1:n.277+21098A>G

Variant summary

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

The ENST00000715761.1(LINC01340):​n.277+21098A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,100 control chromosomes in the GnomAD database, including 1,063 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 0.083 (1063 hom., cov: 32)
• Consequence: LINC01340 ENST00000715761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 1 publications found

Genes affected

LINC01340 (HGNC:50550): (long intergenic non-protein coding RNA 1340)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715761.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01340	ENST00000715761.1		n.277+21098A>G		intron	N/A
	LINC01340	ENST00000746238.1		n.382+21098A>G		intron	N/A
	LINC01340	ENST00000746239.1		n.362+21098A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12601 AN: 151982 Hom.: 1058 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.0685

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

GnomAD4 genome AF: 0.0832 AC: 12651 AN: 152100 Hom.: 1063 Cov.: 32 AF XY: 0.0820 AC XY: 6101 AN XY: 74370

African (AFR) AF: 0.214 AC: 8884 AN: 41462

American (AMR) AF: 0.0532 AC: 812 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.0905 AC: 467 AN: 5162

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4820

European-Finnish (FIN) AF: 0.0437 AC: 464 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0234 AC: 1589 AN: 67998

Other (OTH) AF: 0.0697 AC: 147 AN: 2110

Alfa AF: 0.0386 Hom.: 139

Bravo AF: 0.0915

Asia WGS AF: 0.0700 AC: 244 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.017
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1560326; hg19: chr5-97027486;