rs7999075

Variant names:

• chr13-22046068-C-A
• rs7999075
• ENST00000631321.1:n.410+4684C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-22046068-C-A
• chr13-22046068-C-G
• chr13-22046068-C-T

Variant summary

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

The ENST00000631321.1(LINC00540):​n.410+4684C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,228 control chromosomes in the GnomAD database, including 59,425 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 0.88 (59425 hom., cov: 33)
• Consequence: LINC00540 ENST00000631321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 4 publications found

Genes affected

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

LOC105370108 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370108	XR_007063716.1	n.414+4684C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000631321.1	n.410+4684C>A		intron_variant	Intron 1 of 1	2
LINC00540	ENST00000657205.1	n.413+4684C>A		intron_variant	Intron 1 of 3
LINC00540	ENST00000690279.2	n.410+4684C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134192 AN: 152110 Hom.: 59388 Cov.: 33

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.882 AC: 134286 AN: 152228 Hom.: 59425 Cov.: 33 AF XY: 0.887 AC XY: 66034 AN XY: 74432

African (AFR) AF: 0.822 AC: 34087 AN: 41488

American (AMR) AF: 0.865 AC: 13228 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3075 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4980 AN: 5178

South Asian (SAS) AF: 0.942 AC: 4549 AN: 4830

European-Finnish (FIN) AF: 0.962 AC: 10214 AN: 10620

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61217 AN: 68030

Other (OTH) AF: 0.883 AC: 1864 AN: 2112

Alfa AF: 0.890 Hom.: 151777

Bravo AF: 0.871

Asia WGS AF: 0.929 AC: 3232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.41
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7999075; hg19: chr13-22620207;