rs9510008

chr13-22165121-C-T

Variant summary

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

The ENST00000631321.1(LINC00540):n.411-109402C>T 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 0.181 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 ENST00000631321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

LINC00540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00540	ENST00000631321.1	n.411-109402C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.0762

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.157

Alfa AF: 0.121 Hom.: 2197

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9510008; hg19: chr13-22739260;