rs7318731

Variant names:

• chr13-22135531-A-C
• rs7318731
• ENST00000611481.1:n.165+27897A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-22135531-A-C
• chr13-22135531-A-G
• chr13-22135531-A-T

Variant summary

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

The ENST00000611481.1(LINC00540):​n.165+27897A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,152 control chromosomes in the GnomAD database, including 28,962 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 0.61 (28962 hom., cov: 33)
• Consequence: LINC00540 ENST00000611481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 14 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370108	XR_001749777.2	n.2669-19736A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000611481.1	n.165+27897A>C		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.410+94147A>C		intron_variant	Intron 1 of 1	2
LINC00540	ENST00000657205.1	n.414-48402A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93413 AN: 152034 Hom.: 28944 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.614 AC: 93481 AN: 152152 Hom.: 28962 Cov.: 33 AF XY: 0.625 AC XY: 46507 AN XY: 74382

African (AFR) AF: 0.640 AC: 26580 AN: 41508

American (AMR) AF: 0.634 AC: 9704 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1716 AN: 3472

East Asian (EAS) AF: 0.687 AC: 3551 AN: 5170

South Asian (SAS) AF: 0.660 AC: 3179 AN: 4820

European-Finnish (FIN) AF: 0.769 AC: 8145 AN: 10592

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38887 AN: 67972

Other (OTH) AF: 0.590 AC: 1248 AN: 2116

Alfa AF: 0.582 Hom.: 120603

Bravo AF: 0.604

Asia WGS AF: 0.672 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.66
DANN	Benign	0.47
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs7318731; hg19: chr13-22709670;