ENST00000813770.1:n.97-10239G>T

Variant names:

• chr3-30538043-C-A
• rs28708846
• ENST00000813770.1:n.97-10239G>T

Variant summary

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

The ENST00000813770.1(ENSG00000227549):​n.97-10239G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0588 in 152,208 control chromosomes in the GnomAD database, including 664 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 0.059 (664 hom., cov: 32)
• Consequence: ENSG00000227549 ENST00000813770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 1 publications found

Genes affected

ENSG00000227549 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227549	ENST00000813770.1	n.97-10239G>T		intron_variant	Intron 1 of 2
ENSG00000227549	ENST00000813771.1	n.126-10239G>T		intron_variant	Intron 1 of 1
ENSG00000227549	ENST00000813772.1	n.110-7983G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8937 AN: 152090 Hom.: 664 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0475

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00222

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0588 AC: 8946 AN: 152208 Hom.: 664 Cov.: 32 AF XY: 0.0599 AC XY: 4459 AN XY: 74412

African (AFR) AF: 0.166 AC: 6885 AN: 41496

American (AMR) AF: 0.0471 AC: 721 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.0899 AC: 466 AN: 5186

South Asian (SAS) AF: 0.0102 AC: 49 AN: 4820

European-Finnish (FIN) AF: 0.0521 AC: 552 AN: 10596

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00222 AC: 151 AN: 68032

Other (OTH) AF: 0.0442 AC: 93 AN: 2106

Alfa AF: 0.0187 Hom.: 226

Bravo AF: 0.0647

Asia WGS AF: 0.0750 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.45
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs28708846; hg19: chr3-30579535;