rs7334307

Variant names:

• chr13-42464957-G-A
• rs7334307
• ENST00000637043.2:n.337-20512G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-42464957-G-A
• chr13-42464957-G-C

Variant summary

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

The ENST00000637043.2(LINC02341):​n.337-20512G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,964 control chromosomes in the GnomAD database, including 6,886 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 0.29 (6886 hom., cov: 32)
• Consequence: LINC02341 ENST00000637043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 publications found

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637043.2. 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
	LINC02341	NR_135319.1		n.337-20512G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637043.2	TSL:3	n.337-20512G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43509 AN: 151846 Hom.: 6876 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.287 AC: 43555 AN: 151964 Hom.: 6886 Cov.: 32 AF XY: 0.286 AC XY: 21209 AN XY: 74278

African (AFR) AF: 0.355 AC: 14706 AN: 41418

American (AMR) AF: 0.378 AC: 5770 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2824 AN: 5166

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4812

European-Finnish (FIN) AF: 0.166 AC: 1751 AN: 10548

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.230 AC: 15622 AN: 67974

Other (OTH) AF: 0.304 AC: 641 AN: 2110

Alfa AF: 0.274 Hom.: 1057

Bravo AF: 0.311

Asia WGS AF: 0.349 AC: 1214 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.48
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7334307; hg19: chr13-43039093;