9-16368734-G-T

Variant names:

• chr9-16368734-G-T
• rs7864648
• ENST00000648575.1:n.173+31686C>A

Variant summary

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

The ENST00000648575.1(LINC03041):​n.173+31686C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,940 control chromosomes in the GnomAD database, including 8,402 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 0.33 (8402 hom., cov: 32)
• Consequence: LINC03041 ENST00000648575.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 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
LINC03041	ENST00000648575.1	n.173+31686C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50207 AN: 151820 Hom.: 8405 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.331 AC: 50222 AN: 151940 Hom.: 8402 Cov.: 32 AF XY: 0.335 AC XY: 24887 AN XY: 74250

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.313

Alfa AF: 0.317 Hom.: 12085

Bravo AF: 0.321

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7864648; hg19: chr9-16368732;