rs7999075

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000631321.1(LINC00540):​n.410+4684C>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

LINC00540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105370108	XR_007063716.1	n.414+4684C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000631321.1	n.410+4684C>A		intron_variant, non_coding_transcript_variant		2
LINC00540	ENST00000657205.1	n.413+4684C>A		intron_variant, non_coding_transcript_variant
LINC00540	ENST00000690279.1	n.410+4684C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.942

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.883

Alfa AF: 0.893 Hom.: 56598

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7999075; hg19: chr13-22620207;