rs1330950

Positions:

• chr13-106686453-C-A
• chr13-106686453-C-T

Variant summary

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

The ENST00000663663.1(LINC00551):​n.91-10804C>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 0.617 in 152,114 control chromosomes in the GnomAD database, including 30,464 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 0.62 (30464 hom., cov: 33)
• Consequence: LINC00551 ENST00000663663.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

Genes affected

LINC00551 (HGNC:43691): (ARGLU1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00551	ENST00000663663.1	n.91-10804C>A		intron_variant, non_coding_transcript_variant
LINC00551	ENST00000667614.1	n.133-10804C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93795 AN: 151996 Hom.: 30421 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.617 AC: 93879 AN: 152114 Hom.: 30464 Cov.: 33 AF XY: 0.608 AC XY: 45195 AN XY: 74350

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.623

Alfa AF: 0.563 Hom.: 47033

Bravo AF: 0.633

Asia WGS AF: 0.470 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.57
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330950; hg19: chr13-107338801;