rs7332465

Variant names:

• chr13-22095568-G-A
• rs7332465
• XR_007063715.1:n.24400G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-22095568-G-A
• chr13-22095568-G-C

Variant summary

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

The XR_007063715.1(LOC105370108):​n.24400G>A 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 0.648 in 152,080 control chromosomes in the GnomAD database, including 34,701 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 0.65 (34701 hom., cov: 32)
• Consequence: LOC105370108 XR_007063715.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631321.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00540	ENST00000631321.1	TSL:2	n.410+54184G>A		intron	N/A
	LINC00540	ENST00000657205.1		n.413+54184G>A		intron	N/A
	LINC00540	ENST00000690279.2		n.411-17230G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98453 AN: 151962 Hom.: 34695 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.648 AC: 98481 AN: 152080 Hom.: 34701 Cov.: 32 AF XY: 0.647 AC XY: 48122 AN XY: 74362

African (AFR) AF: 0.344 AC: 14243 AN: 41460

American (AMR) AF: 0.710 AC: 10843 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2581 AN: 3470

East Asian (EAS) AF: 0.698 AC: 3610 AN: 5170

South Asian (SAS) AF: 0.733 AC: 3531 AN: 4818

European-Finnish (FIN) AF: 0.762 AC: 8052 AN: 10568

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53226 AN: 68000

Other (OTH) AF: 0.675 AC: 1422 AN: 2108

Alfa AF: 0.743 Hom.: 69144

Bravo AF: 0.630

Asia WGS AF: 0.683 AC: 2375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.42
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs7332465; hg19: chr13-22669707;