rs10962339

Variant names:

• chr9-16222146-A-C
• rs10962339
• ENST00000380685.5:n.84-6247T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC03041	NR_171034.1	n.84-6247T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03041	ENST00000380685.5	n.84-6247T>G		intron_variant	Intron 1 of 3	2
LINC03041	ENST00000433347.2	n.76-6247T>G		intron_variant	Intron 1 of 3	3
LINC03041	ENST00000648575.1	n.174-6247T>G		intron_variant	Intron 2 of 3
LINC03041	ENST00000824553.1	n.88-6247T>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.286 AC: 11846 AN: 41464

American (AMR) AF: 0.166 AC: 2532 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3464

East Asian (EAS) AF: 0.123 AC: 633 AN: 5160

South Asian (SAS) AF: 0.254 AC: 1219 AN: 4806

European-Finnish (FIN) AF: 0.124 AC: 1314 AN: 10594

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10934 AN: 67978

Other (OTH) AF: 0.181 AC: 382 AN: 2114

Alfa AF: 0.162 Hom.: 2165

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
PhyloP100		1.0

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

Other links and lift over

dbSNP: rs10962339; hg19: chr9-16222144;