rs10770612

Variant names:

• chr12-20077705-A-G
• rs10770612
• ENST00000716354.1:n.4576-21047A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-20077705-A-G
• chr12-20077705-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_040098.1(LINC02398):​n.410-21047A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,134 control chromosomes in the GnomAD database, including 2,873 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 0.17 (2873 hom., cov: 32)
• Consequence: LINC02398 NR_040098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.18
• Publications: 33 publications found

Genes affected

ENSG00000255910 (HGNC:):

LINC02398 (HGNC:53325): (long intergenic non-protein coding RNA 2398)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_040098.1. 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
	LINC02398	NR_040098.1		n.410-21047A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255910	ENST00000716354.1		n.4576-21047A>G		intron	N/A
	ENSG00000255910	ENST00000716355.1		n.5562-21047A>G		intron	N/A
	ENSG00000255910	ENST00000716356.1		n.5908-21047A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25880 AN: 152016 Hom.: 2868 Cov.: 32

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.170 AC: 25894 AN: 152134 Hom.: 2873 Cov.: 32 AF XY: 0.176 AC XY: 13095 AN XY: 74368

African (AFR) AF: 0.0391 AC: 1625 AN: 41526

American (AMR) AF: 0.234 AC: 3577 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 581 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1801 AN: 5170

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4820

European-Finnish (FIN) AF: 0.236 AC: 2501 AN: 10576

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

European-Non Finnish (NFE) AF: 0.201 AC: 13655 AN: 67978

Other (OTH) AF: 0.167 AC: 353 AN: 2110

Alfa AF: 0.198 Hom.: 12851

Bravo AF: 0.167

Asia WGS AF: 0.325 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	18
DANN	Benign	0.86
PhyloP100		3.2

Splicing

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

Other links and lift over

dbSNP: rs10770612; hg19: chr12-20230639;