rs9510008

Variant names:

• chr13-22165121-C-T
• rs9510008
• ENST00000611481.1:n.165+57487C>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+57487C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,774 control chromosomes in the GnomAD database, including 3,245 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 0.18 (3245 hom., cov: 32)
• Consequence: LINC00540 ENST00000611481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 2 publications found

Genes affected

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000611481.1	n.165+57487C>T		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.411-109402C>T		intron_variant	Intron 1 of 1	2
LINC00540	ENST00000657205.1	n.414-18812C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27453 AN: 151656 Hom.: 3234 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0762

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.181 AC: 27514 AN: 151774 Hom.: 3245 Cov.: 32 AF XY: 0.181 AC XY: 13456 AN XY: 74168

African (AFR) AF: 0.317 AC: 13131 AN: 41372

American (AMR) AF: 0.231 AC: 3518 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0762 AC: 264 AN: 3466

East Asian (EAS) AF: 0.149 AC: 767 AN: 5158

South Asian (SAS) AF: 0.143 AC: 689 AN: 4814

European-Finnish (FIN) AF: 0.0993 AC: 1046 AN: 10532

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7591 AN: 67880

Other (OTH) AF: 0.157 AC: 330 AN: 2104

Alfa AF: 0.130 Hom.: 4106

Bravo AF: 0.196

Asia WGS AF: 0.175 AC: 606 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.12
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs9510008; hg19: chr13-22739260;