rs10773338

Variant names:

• chr12-126919857-G-A
• rs10773338
• ENST00000512624.6:n.1114+2850C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-126919857-G-A
• chr12-126919857-G-T

Variant summary

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

The ENST00000512624.6(LINC02405):​n.1114+2850C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,012 control chromosomes in the GnomAD database, including 35,565 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 0.65 (35565 hom., cov: 32)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 4 publications found

Genes affected

LINC02405 (HGNC:53333): (long intergenic non-protein coding RNA 2405)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02405	NR_104646.1	n.1114+2850C>T		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02405	ENST00000512624.6	n.1114+2850C>T		intron_variant	Intron 6 of 6	1
LINC02405	ENST00000651439.2	n.1138+2850C>T		intron_variant	Intron 7 of 7
LINC02405	ENST00000656033.1	n.1106+2850C>T		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98894 AN: 151894 Hom.: 35575 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.651 AC: 98887 AN: 152012 Hom.: 35565 Cov.: 32 AF XY: 0.644 AC XY: 47875 AN XY: 74308

African (AFR) AF: 0.357 AC: 14781 AN: 41406

American (AMR) AF: 0.565 AC: 8625 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2249 AN: 5164

South Asian (SAS) AF: 0.735 AC: 3543 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8188 AN: 10562

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56659 AN: 67992

Other (OTH) AF: 0.653 AC: 1379 AN: 2112

Alfa AF: 0.766 Hom.: 35437

Bravo AF: 0.619

Asia WGS AF: 0.579 AC: 2010 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10773338; hg19: chr12-127404403;