9-16368734-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648575.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03041	ENST00000648575.1		n.173+31686C>A		intron	N/A

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

African (AFR) AF: 0.332 AC: 13768 AN: 41440

American (AMR) AF: 0.298 AC: 4548 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1595 AN: 5158

South Asian (SAS) AF: 0.464 AC: 2229 AN: 4802

European-Finnish (FIN) AF: 0.360 AC: 3796 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22170 AN: 67936

Other (OTH) AF: 0.313 AC: 660 AN: 2112

Alfa AF: 0.322 Hom.: 28170

Bravo AF: 0.321

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs7864648; hg19: chr9-16368732;