rs4301033

Variant names:

• chr3-150324831-G-A
• rs4301033
• ENST00000692847.3:n.76+6116C>T

Variant summary

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

The ENST00000692847.3(LINC01214):​n.76+6116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,172 control chromosomes in the GnomAD database, including 1,239 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 0.11 (1239 hom., cov: 32)
• Consequence: LINC01214 ENST00000692847.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.54
• Publications: 16 publications found

Genes affected

LINC01214 (HGNC:49650): (long intergenic non-protein coding RNA 1214)

ENSG00000297695 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692847.3. 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
	LINC01214	ENST00000692847.3		n.76+6116C>T		intron	N/A
	LINC01214	ENST00000716186.1		n.41+6116C>T		intron	N/A
	LINC01214	ENST00000716187.1		n.623+16275C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17233 AN: 152054 Hom.: 1237 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0556

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.113 AC: 17255 AN: 152172 Hom.: 1239 Cov.: 32 AF XY: 0.110 AC XY: 8190 AN XY: 74404

African (AFR) AF: 0.194 AC: 8054 AN: 41494

American (AMR) AF: 0.0787 AC: 1204 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0552 AC: 266 AN: 4816

European-Finnish (FIN) AF: 0.0672 AC: 712 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0915 AC: 6224 AN: 68004

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.0983 Hom.: 3436

Bravo AF: 0.120

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		3.5

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: rs4301033;

hg19: chr3-150042618;