rs10821312

Variant names:

• chr9-94182299-A-G
• rs10821312
• ENST00000416309.6:n.165-4568T>C

Variant summary

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

The ENST00000651632.1(LINC02603):​n.927T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,166 control chromosomes in the GnomAD database, including 3,128 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 0.19 (3128 hom., cov: 32)
• Consequence: LINC02603 ENST00000651632.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 6 publications found

Genes affected

LINC02603 (HGNC:37186): (long intergenic non-protein coding RNA 2603)

MIRLET7A1HG (HGNC:53970): (miRlet-7a-1/let-7f-1/let-7d cluster host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651632.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02603	NR_046163.1		n.188-4568T>C		intron	N/A
	LINC02603	NR_046165.1		n.129-4568T>C		intron	N/A
	LINC02603	NR_160773.1		n.256-4568T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02603	ENST00000416309.6	TSL:1	n.165-4568T>C		intron	N/A
	LINC02603	ENST00000602602.3	TSL:1	n.159-4568T>C		intron	N/A
	LINC02603	ENST00000651632.1		n.927T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29364 AN: 152048 Hom.: 3125 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.193 AC: 29392 AN: 152166 Hom.: 3128 Cov.: 32 AF XY: 0.191 AC XY: 14202 AN XY: 74396

African (AFR) AF: 0.280 AC: 11621 AN: 41496

American (AMR) AF: 0.136 AC: 2080 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5172

South Asian (SAS) AF: 0.131 AC: 633 AN: 4826

European-Finnish (FIN) AF: 0.204 AC: 2165 AN: 10592

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11778 AN: 67996

Other (OTH) AF: 0.169 AC: 357 AN: 2108

Alfa AF: 0.175 Hom.: 10075

Bravo AF: 0.190

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10821312; hg19: chr9-96944581; COSMIC: COSV63010122;