rs10821312

Positions:

• chr9-94182299-A-G

Variant summary

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

The NR_160773.1(LINC02603):​n.256-4568T>C 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 0.193 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 NR_160773.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02603	NR_160773.1	n.256-4568T>C		intron_variant, non_coding_transcript_variant
MIRLET7A1HG	NR_170278.1	n.328-964A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02603	ENST00000668497.1	n.406-4568T>C		intron_variant, non_coding_transcript_variant
MIRLET7A1HG	ENST00000710611.1	n.209+6334A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.169

Alfa AF: 0.170 Hom.: 4384

Bravo AF: 0.190

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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