chr9-31372585-A-C

Variant names:

• chr9-31372585-A-C
• rs10970305
• ENST00000562065.1:n.133-386T>G

Variant summary

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

The ENST00000562065.1(LINC01243):​n.133-386T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,960 control chromosomes in the GnomAD database, including 27,997 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 0.60 (27997 hom., cov: 32)
• Consequence: LINC01243 ENST00000562065.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 3 publications found

Genes affected

LINC01243 (HGNC:49814): (long intergenic non-protein coding RNA 1243)

ENSG00000297756 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01243	NR_135134.1	n.133-386T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01243	ENST00000562065.1	n.133-386T>G		intron_variant	Intron 1 of 1	1
ENSG00000297756	ENST00000750803.1	n.120-35427T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90903 AN: 151842 Hom.: 27937 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.599 AC: 91025 AN: 151960 Hom.: 27997 Cov.: 32 AF XY: 0.607 AC XY: 45044 AN XY: 74250

African (AFR) AF: 0.720 AC: 29836 AN: 41466

American (AMR) AF: 0.631 AC: 9637 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1818 AN: 3472

East Asian (EAS) AF: 0.791 AC: 4085 AN: 5162

South Asian (SAS) AF: 0.706 AC: 3403 AN: 4818

European-Finnish (FIN) AF: 0.575 AC: 6053 AN: 10526

Middle Eastern (MID) AF: 0.566 AC: 164 AN: 290

European-Non Finnish (NFE) AF: 0.506 AC: 34345 AN: 67940

Other (OTH) AF: 0.571 AC: 1206 AN: 2112

Alfa AF: 0.534 Hom.: 31849

Bravo AF: 0.609

Asia WGS AF: 0.758 AC: 2632 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.73
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs10970305; hg19: chr9-31372583;