chr9-93497300-C-T

Position:

• chr9-93497300-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014612.5(FAM120A):​c.805-171C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,120 control chromosomes in the GnomAD database, including 7,032 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (7032 hom., cov: 33)
• Consequence: FAM120A NM_014612.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.731

Genes affected

FAM120A (HGNC:13247): (family with sequence similarity 120 member A) Enables RNA binding activity. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 9-93497300-C-T is Benign according to our data. Variant chr9-93497300-C-T is described in ClinVar as [Benign]. Clinvar id is 1275524.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM120A	NM_014612.5	c.805-171C>T		intron_variant		ENST00000277165.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM120A	ENST00000277165.11	c.805-171C>T		intron_variant		1	NM_014612.5	P3
FAM120A	ENST00000375389.7	c.805-171C>T		intron_variant		1
FAM120A	ENST00000446420.2	c.337-171C>T		intron_variant		5
FAM120A	ENST00000698944.1	c.805-171C>T		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42534 AN: 152002 Hom.: 7033 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.280 AC: 42539 AN: 152120 Hom.: 7032 Cov.: 33 AF XY: 0.281 AC XY: 20889 AN XY: 74342

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.292

Alfa AF: 0.314 Hom.: 1281

Bravo AF: 0.273

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.96
DANN	Benign	0.55

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: rs2297376; hg19: chr9-96259582;