rs10514921

Variant names:

• chr5-61769270-G-A
• rs10514921
• ENST00000667197.1:n.813+13326G>A

Variant summary

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

The ENST00000667197.1(LINC03122):​n.813+13326G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0329 in 152,246 control chromosomes in the GnomAD database, including 141 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 0.033 (141 hom., cov: 32)
• Consequence: LINC03122 ENST00000667197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787
• Publications: 1 publications found

Genes affected

LINC03122 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000303846 (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 (NFE) allele frequency at 95% confidence interval = 0.0506 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
LINC03122	ENST00000667197.1	n.813+13326G>A		intron_variant	Intron 6 of 6
LINC03122	ENST00000797193.1	n.570+13326G>A		intron_variant	Intron 5 of 10
LINC03122	ENST00000797195.1	n.347-11970G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0329 AC: 5006 AN: 152128 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.00821

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00974

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0521

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0329 AC: 5007 AN: 152246 Hom.: 141 Cov.: 32 AF XY: 0.0304 AC XY: 2263 AN XY: 74450

African (AFR) AF: 0.00818 AC: 340 AN: 41554

American (AMR) AF: 0.0268 AC: 410 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00995 AC: 48 AN: 4822

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10602

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0521 AC: 3542 AN: 68010

Other (OTH) AF: 0.0369 AC: 78 AN: 2112

Alfa AF: 0.0481 Hom.: 260

Bravo AF: 0.0336

Asia WGS AF: 0.00664 AC: 23 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	2.7
DANN	Benign	0.46
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10514921; hg19: chr5-61065097;