ENST00000436786.2:n.622+47457A>G

Variant names:

• chr9-22770887-A-G
• rs10811771
• ENST00000436786.2:n.622+47457A>G

Variant summary

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

The ENST00000436786.2(LINC01239):​n.622+47457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,834 control chromosomes in the GnomAD database, including 8,236 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 0.31 (8236 hom., cov: 31)
• Consequence: LINC01239 ENST00000436786.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 12 publications found

Genes affected

LINC01239 (HGNC:49796): (long intergenic non-protein coding RNA 1239)

ENSG00000284418 (HGNC:58153):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01239	NR_038977.1	n.524+47457A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01239	ENST00000436786.2	n.622+47457A>G		intron_variant	Intron 4 of 5	2
ENSG00000284418	ENST00000640003.1	n.559-5611T>C		intron_variant	Intron 5 of 9	5
ENSG00000284418	ENST00000764217.1	n.241-29367T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47141 AN: 151716 Hom.: 8235 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.311 AC: 47145 AN: 151834 Hom.: 8236 Cov.: 31 AF XY: 0.311 AC XY: 23060 AN XY: 74194

African (AFR) AF: 0.168 AC: 6966 AN: 41444

American (AMR) AF: 0.436 AC: 6606 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1517 AN: 3462

East Asian (EAS) AF: 0.150 AC: 772 AN: 5132

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4820

European-Finnish (FIN) AF: 0.279 AC: 2949 AN: 10584

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25299 AN: 67916

Other (OTH) AF: 0.317 AC: 669 AN: 2110

Alfa AF: 0.352 Hom.: 26173

Bravo AF: 0.313

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.59
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10811771; hg19: chr9-22770886;