rs9321439

Variant names:

• chr6-134407056-T-A
• rs9321439
• ENST00000431422.3:n.54-30259T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-134407056-T-A
• chr6-134407056-T-G

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-30259T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,142 control chromosomes in the GnomAD database, including 15,116 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 0.35 (15116 hom., cov: 33)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01010	ENST00000431422.3	n.54-30259T>A		intron_variant	Intron 1 of 3	2
LINC01010	ENST00000660399.1	n.54-57685T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52848 AN: 152024 Hom.: 15066 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.348 AC: 52940 AN: 152142 Hom.: 15116 Cov.: 33 AF XY: 0.339 AC XY: 25190 AN XY: 74386

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.354

Alfa AF: 0.270 Hom.: 1219

Bravo AF: 0.378

Asia WGS AF: 0.199 AC: 693 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321439; hg19: chr6-134728194;