rs2207337

Variant names:

• chr6-29232468-T-A
• rs2207337
• ENST00000733451.1:n.48A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-29232468-T-A
• chr6-29232468-T-C

Variant summary

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

The ENST00000733451.1(ENSG00000295878):​n.48A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,934 control chromosomes in the GnomAD database, including 25,104 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 0.56 (25104 hom., cov: 31)
• Consequence: ENSG00000295878 ENST00000733451.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 5 publications found

Genes affected

ENSG00000295878 (HGNC:):

LINC03003 (HGNC:56126): (long intergenic non-protein coding RNA 3003)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733451.1. 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
	LINC03003	NR_134629.1		n.79+8417T>A		intron	N/A
	LINC03003	NR_134630.1		n.79+8417T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295878	ENST00000733451.1		n.48A>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000295878	ENST00000733452.1		n.143A>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000295878	ENST00000733453.1		n.163A>T		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84430 AN: 151816 Hom.: 25107 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.556 AC: 84446 AN: 151934 Hom.: 25104 Cov.: 31 AF XY: 0.564 AC XY: 41894 AN XY: 74262

African (AFR) AF: 0.339 AC: 14026 AN: 41406

American (AMR) AF: 0.569 AC: 8680 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2438 AN: 5154

South Asian (SAS) AF: 0.626 AC: 3006 AN: 4804

European-Finnish (FIN) AF: 0.772 AC: 8151 AN: 10562

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44170 AN: 67974

Other (OTH) AF: 0.547 AC: 1150 AN: 2102

Alfa AF: 0.605 Hom.: 3603

Bravo AF: 0.522

Asia WGS AF: 0.607 AC: 2111 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.8
DANN	Benign	0.87
PhyloP100		0.029

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: rs2207337;

hg19: chr6-29200245;