2-85538814-G-T

Variant names:

• chr2-85538814-G-T
• rs60749033
• ENST00000667933.3:n.297C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BS1 BS2

The NR_038942.1(PARTICL):​n.73C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00931 in 151,846 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0093 (20 hom., cov: 33)
• Consequence: PARTICL NR_038942.1 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.12
• Publications: 0 publications found

Genes affected

PARTICL (HGNC:50886): (promoter of MAT2A antisense radiation-induced circulating long non-coding RNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BP6: Variant 2-85538814-G-T is Benign according to our data. Variant chr2-85538814-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1317699.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00931 (1413/151846) while in subpopulation AFR AF = 0.0326 (1350/41388). AF 95% confidence interval is 0.0312. There are 20 homozygotes in GnomAd4. There are 653 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 20 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARTICL	NR_038942.1	n.73C>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARTICL	ENST00000667933.3	n.297C>A		non_coding_transcript_exon_variant	Exon 1 of 1
PARTICL	ENST00000737206.1	n.4C>A		non_coding_transcript_exon_variant	Exon 1 of 2
PARTICL	ENST00000737207.1	n.-1C>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.00929 AC: 1409 AN: 151728 Hom.: 20 Cov.: 33

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00315

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000883

Gnomad OTH AF: 0.00431

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

GnomAD4 genome AF: 0.00931 AC: 1413 AN: 151846 Hom.: 20 Cov.: 33 AF XY: 0.00880 AC XY: 653 AN XY: 74208

African (AFR) AF: 0.0326 AC: 1350 AN: 41388

American (AMR) AF: 0.00314 AC: 48 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5076

South Asian (SAS) AF: 0.00 AC: 0 AN: 4800

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 286

European-Non Finnish (NFE) AF: 0.0000883 AC: 6 AN: 67928

Other (OTH) AF: 0.00427 AC: 9 AN: 2110

Alfa AF: 0.00312 Hom.: 1

Bravo AF: 0.0105

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 28, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	20
DANN	Benign	0.89
PhyloP100		2.1
PromoterAI		-0.044	Neutral

Splicing

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

Other links and lift over

dbSNP: rs60749033; hg19: chr2-85765937;