2-8312367-C-T

Variant names:

• chr2-8312367-C-T
• rs3102960
• ENST00000430192.5:n.89+12175G>A

Variant summary

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

The ENST00000430192.5(LINC00299):​n.89+12175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,136 control chromosomes in the GnomAD database, including 54,556 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 0.84 (54556 hom., cov: 31)
• Consequence: LINC00299 ENST00000430192.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765
• Publications: 6 publications found

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430192.5. 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
	LINC00299	NR_034135.1		n.329+12175G>A		intron	N/A
	LINC00299	NR_152741.1		n.453+359G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00299	ENST00000430192.5	TSL:1	n.89+12175G>A		intron	N/A
	LINC00299	ENST00000442956.1	TSL:2	n.453+359G>A		intron	N/A
	LINC00299	ENST00000668369.1		n.99-9942G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128207 AN: 152018 Hom.: 54494 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.844 AC: 128330 AN: 152136 Hom.: 54556 Cov.: 31 AF XY: 0.840 AC XY: 62459 AN XY: 74378

African (AFR) AF: 0.951 AC: 39467 AN: 41520

American (AMR) AF: 0.876 AC: 13404 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2584 AN: 3472

East Asian (EAS) AF: 0.856 AC: 4418 AN: 5162

South Asian (SAS) AF: 0.741 AC: 3569 AN: 4818

European-Finnish (FIN) AF: 0.769 AC: 8141 AN: 10588

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54116 AN: 67958

Other (OTH) AF: 0.838 AC: 1769 AN: 2112

Alfa AF: 0.813 Hom.: 62400

Bravo AF: 0.857

Asia WGS AF: 0.847 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.20
PhyloP100		-0.77

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: rs3102960;

hg19: chr2-8452497;