ENST00000450746.3:n.113-2709A>G

Variant names:

• chr3-30521994-A-G
• rs9850953
• ENST00000450746.3:n.113-2709A>G

Variant summary

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

The ENST00000450746.3(LINC01985):​n.113-2709A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,034 control chromosomes in the GnomAD database, including 13,310 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 0.40 (13310 hom., cov: 32)
• Consequence: LINC01985 ENST00000450746.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 2 publications found

Genes affected

LINC01985 (HGNC:52816): (long intergenic non-protein coding RNA 1985)

ENSG00000227549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450746.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01985	NR_147054.1		n.91-2713A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01985	ENST00000450746.3	TSL:3	n.113-2709A>G		intron	N/A
	ENSG00000227549	ENST00000654195.1		n.473-13T>C		intron	N/A
	LINC01985	ENST00000657930.2		n.335-2709A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60128 AN: 151916 Hom.: 13268 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.396 AC: 60221 AN: 152034 Hom.: 13310 Cov.: 32 AF XY: 0.398 AC XY: 29619 AN XY: 74332

African (AFR) AF: 0.607 AC: 25147 AN: 41444

American (AMR) AF: 0.309 AC: 4717 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2633 AN: 5166

South Asian (SAS) AF: 0.355 AC: 1711 AN: 4818

European-Finnish (FIN) AF: 0.337 AC: 3566 AN: 10580

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20135 AN: 67974

Other (OTH) AF: 0.379 AC: 801 AN: 2112

Alfa AF: 0.182 Hom.: 344

Bravo AF: 0.403

Asia WGS AF: 0.452 AC: 1572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.44
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs9850953; hg19: chr3-30563486;