rs9646096

Variant names:

• chr13-37491309-A-C
• rs9646096
• ENST00000827904.1:n.103-6916T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000827904.1(LINC01048):​n.103-6916T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 152,258 control chromosomes in the GnomAD database, including 237 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 0.050 (237 hom., cov: 32)
• Consequence: LINC01048 ENST00000827904.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.970
• Publications: 9 publications found

Genes affected

LINC01048 (HGNC:49042): (long intergenic non-protein coding RNA 1048)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827904.1. 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
	LINC01048	ENST00000827904.1		n.103-6916T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 7640 AN: 152140 Hom.: 235 Cov.: 32

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0503 AC: 7656 AN: 152258 Hom.: 237 Cov.: 32 AF XY: 0.0501 AC XY: 3729 AN XY: 74430

African (AFR) AF: 0.0572 AC: 2380 AN: 41574

American (AMR) AF: 0.0835 AC: 1275 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0551 AC: 191 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4832

European-Finnish (FIN) AF: 0.0426 AC: 452 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3086 AN: 68020

Other (OTH) AF: 0.0687 AC: 145 AN: 2112

Alfa AF: 0.0454 Hom.: 105

Bravo AF: 0.0531

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.63
PhyloP100		0.97

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9646096;

hg19: chr13-38065446;