rs10962339

Positions:

• chr9-16222146-A-C
• chr9-16222146-A-G

Variant summary

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

The ENST00000380685.5(LINC03041):​n.84-6247T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,066 control chromosomes in the GnomAD database, including 3,151 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 0.20 (3151 hom., cov: 32)
• Consequence: LINC03041 ENST00000380685.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

LINC03041 (HGNC:19054): (long intergenic non-protein coding RNA 3041)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03041	NR_171034.1	n.84-6247T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03041	ENST00000380685.5	n.84-6247T>G		intron_variant		2
LINC03041	ENST00000433347.2	n.76-6247T>G		intron_variant		3
LINC03041	ENST00000648575.1	n.174-6247T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29635 AN: 151948 Hom.: 3146 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.195 AC: 29675 AN: 152066 Hom.: 3151 Cov.: 32 AF XY: 0.194 AC XY: 14436 AN XY: 74326

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.181

Alfa AF: 0.158 Hom.: 1508

Bravo AF: 0.200

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10962339; hg19: chr9-16222144;