13-30873838-A-G

Variant names:

• chr13-30873838-A-G
• rs213617
• ENST00000690833.2:n.272-8722A>G

Variant summary

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

The ENST00000690833.2(LINC00398):​n.272-8722A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,238 control chromosomes in the GnomAD database, including 1,733 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 0.14 (1733 hom., cov: 32)
• Consequence: LINC00398 ENST00000690833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 2 publications found

Genes affected

LINC00398 (HGNC:42727): (long intergenic non-protein coding RNA 398)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690833.2. 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
	LINC00398	ENST00000690833.2		n.272-8722A>G		intron	N/A
	LINC00398	ENST00000715721.1		n.709-8722A>G		intron	N/A
	LINC00398	ENST00000799400.1		n.137-8722A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21410 AN: 152120 Hom.: 1729 Cov.: 32

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.141 AC: 21420 AN: 152238 Hom.: 1733 Cov.: 32 AF XY: 0.144 AC XY: 10727 AN XY: 74428

African (AFR) AF: 0.0540 AC: 2243 AN: 41556

American (AMR) AF: 0.192 AC: 2934 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 845 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1389 AN: 5170

South Asian (SAS) AF: 0.178 AC: 858 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1725 AN: 10592

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10965 AN: 68008

Other (OTH) AF: 0.147 AC: 310 AN: 2116

Alfa AF: 0.153 Hom.: 2564

Bravo AF: 0.141

Asia WGS AF: 0.195 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.51
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs213617; hg19: chr13-31447975;