ENST00000423591.5:c.-274C>A

Variant names:

• chr9-93451378-G-T
• rs115641885
• ENST00000423591.5:c.-274C>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000423591.5(FAM120AOS):​c.-274C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00405 in 1,405,814 control chromosomes in the GnomAD database, including 137 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.018 (74 hom., cov: 32)
  • Exomes 𝑓: 0.0024 (63 hom.)
• Consequence: FAM120AOS ENST00000423591.5 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.627

Genes affected

FAM120AOS (HGNC:23389): (family with sequence similarity 120 member A opposite strand) Differences in the expression level of this gene are associated with the survival rate of those with glioma. [provided by RefSeq, May 2017]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BP6: Variant 9-93451378-G-T is Benign according to our data. Variant chr9-93451378-G-T is described in ClinVar as [Benign]. Clinvar id is 1180290.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120AOS	NM_198841.4	c.563+769C>A		intron_variant	Intron 1 of 2	ENST00000375412.11	NP_942138.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120AOS	ENST00000375412.11	c.563+769C>A		intron_variant	Intron 1 of 2	1	NM_198841.4	ENSP00000364561.5

Frequencies

GnomAD3 genomes AF: 0.0180 AC: 2701 AN: 149962 Hom.: 73 Cov.: 32

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00691

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00105

Gnomad OTH AF: 0.0151

GnomAD4 exome AF: 0.00238 AC: 2988 AN: 1255736 Hom.: 63 Cov.: 31 AF XY: 0.00221 AC XY: 1341 AN XY: 607500

Gnomad4 AFR exome AF: 0.0671

Gnomad4 AMR exome AF: 0.00631

Gnomad4 ASJ exome AF: 0.00193

Gnomad4 EAS exome AF: 0.0000308

Gnomad4 SAS exome AF: 0.000244

Gnomad4 FIN exome AF: 0.0000334

Gnomad4 NFE exome AF: 0.000717

Gnomad4 OTH exome AF: 0.00560

GnomAD4 genome AF: 0.0180 AC: 2702 AN: 150078 Hom.: 74 Cov.: 32 AF XY: 0.0164 AC XY: 1203 AN XY: 73476

Gnomad4 AFR AF: 0.0625

Gnomad4 AMR AF: 0.00690

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00105

Gnomad4 OTH AF: 0.0149

Alfa AF: 0.000286 Hom.: 0

Bravo AF: 0.0210

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Oct 27, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.9
DANN	Benign	0.75
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs115641885; hg19: chr9-96213660;