chr9-11018077-C-A

Variant names:

• chr9-11018077-C-A
• rs12346562
• ENST00000603198.2:n.281+28458G>T

Variant summary

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

The ENST00000827113.1(LINC03131):​n.158-23812G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,684 control chromosomes in the GnomAD database, including 4,660 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 0.24 (4660 hom., cov: 33)
• Consequence: LINC03131 ENST00000827113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 6 publications found

Genes affected

LINC03131 (HGNC:58088):

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 (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827113.1. 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
	LINC03131	ENST00000603198.2	TSL:6	n.281+28458G>T		intron	N/A
	LINC03131	ENST00000827113.1		n.158-23812G>T		intron	N/A
	LINC03131	ENST00000827114.1		n.159+46892G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36344 AN: 151568 Hom.: 4662 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.240 AC: 36362 AN: 151684 Hom.: 4660 Cov.: 33 AF XY: 0.238 AC XY: 17660 AN XY: 74120

African (AFR) AF: 0.182 AC: 7552 AN: 41396

American (AMR) AF: 0.177 AC: 2701 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.0481 AC: 248 AN: 5158

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4810

European-Finnish (FIN) AF: 0.329 AC: 3433 AN: 10448

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19055 AN: 67868

Other (OTH) AF: 0.271 AC: 568 AN: 2098

Alfa AF: 0.265 Hom.: 18579

Bravo AF: 0.224

Asia WGS AF: 0.150 AC: 522 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.45
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs12346562; hg19: chr9-11018077;