rs7334903

Variant names:

• chr13-22074072-A-G
• rs7334903
• XR_007063715.1:n.2904A>G

Variant summary

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

The XR_007063715.1(LOC105370108):​n.2904A>G 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 0.123 in 152,280 control chromosomes in the GnomAD database, including 2,673 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 0.12 (2673 hom., cov: 33)
• Consequence: LOC105370108 XR_007063715.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 publications found

Genes affected

LOC105370108 (HGNC:):

LINC00540 (HGNC:43673): (long intergenic non-protein coding RNA 540)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370108	XR_007063715.1	n.2904A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105370108	XR_007063716.1	n.1039A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105370108	XR_001749777.2	n.2668+236A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000631321.1	n.410+32688A>G		intron_variant	Intron 1 of 1	2
LINC00540	ENST00000657205.1	n.413+32688A>G		intron_variant	Intron 1 of 3
LINC00540	ENST00000690279.2	n.410+32688A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18728 AN: 152162 Hom.: 2665 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0619

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0993

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

GnomAD4 genome AF: 0.123 AC: 18756 AN: 152280 Hom.: 2673 Cov.: 33 AF XY: 0.119 AC XY: 8876 AN XY: 74482

African (AFR) AF: 0.352 AC: 14606 AN: 41514

American (AMR) AF: 0.0601 AC: 920 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5182

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4824

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10626

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0336 AC: 2285 AN: 68036

Other (OTH) AF: 0.0983 AC: 208 AN: 2116

Alfa AF: 0.124 Hom.: 456

Bravo AF: 0.134

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7334903; hg19: chr13-22648211;