rs7970841

Variant names:

• chr12-30230089-A-C
• rs7970841
• ENST00000824524.1:n.169+14246T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-30230089-A-C
• chr12-30230089-A-G
• chr12-30230089-A-T

Variant summary

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

The ENST00000824524.1(LINC02386):​n.169+14246T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,050 control chromosomes in the GnomAD database, including 44,838 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 0.76 (44838 hom., cov: 31)
• Consequence: LINC02386 ENST00000824524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 3 publications found

Genes affected

LINC02386 (HGNC:53312): (long intergenic non-protein coding RNA 2386)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824524.1. 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
	LINC02386	ENST00000824524.1		n.169+14246T>G		intron	N/A
	LINC02386	ENST00000824525.1		n.223+14246T>G		intron	N/A
	LINC02386	ENST00000824526.1		n.315+2687T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116046 AN: 151932 Hom.: 44784 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.764 AC: 116163 AN: 152050 Hom.: 44838 Cov.: 31 AF XY: 0.765 AC XY: 56794 AN XY: 74284

African (AFR) AF: 0.875 AC: 36340 AN: 41520

American (AMR) AF: 0.797 AC: 12162 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2335 AN: 3470

East Asian (EAS) AF: 0.843 AC: 4354 AN: 5162

South Asian (SAS) AF: 0.789 AC: 3801 AN: 4816

European-Finnish (FIN) AF: 0.675 AC: 7117 AN: 10548

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47489 AN: 67970

Other (OTH) AF: 0.771 AC: 1625 AN: 2108

Alfa AF: 0.715 Hom.: 23033

Bravo AF: 0.780

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7970841; hg19: chr12-30383022;