9-93476449-C-T

Position:

• chr9-93476449-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.804+111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 688,540 control chromosomes in the GnomAD database, including 33,847 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.27 (6591 hom., cov: 32)
  • Exomes 𝑓: 0.31 (27256 hom.)
• Consequence: FAM120A NM_014612.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.130

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=-0.87).
• BP6: Variant 9-93476449-C-T is Benign according to our data. Variant chr9-93476449-C-T is described in ClinVar as [Benign]. Clinvar id is 1244777.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM120A	NM_014612.5	c.804+111C>T		intron_variant		ENST00000277165.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM120A	ENST00000277165.11	c.804+111C>T		intron_variant		1	NM_014612.5	P3
FAM120A	ENST00000375389.7	c.804+111C>T		intron_variant		1
FAM120A	ENST00000446420.2	c.336+111C>T		intron_variant		5
FAM120A	ENST00000698944.1	c.804+111C>T		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40967 AN: 151880 Hom.: 6593 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.309 AC: 165719 AN: 536542 Hom.: 27256 AF XY: 0.303 AC XY: 86047 AN XY: 284432

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.301

Gnomad4 ASJ exome AF: 0.301

Gnomad4 EAS exome AF: 0.471

Gnomad4 SAS exome AF: 0.151

Gnomad4 FIN exome AF: 0.356

Gnomad4 NFE exome AF: 0.325

Gnomad4 OTH exome AF: 0.292

GnomAD4 genome AF: 0.270 AC: 40965 AN: 151998 Hom.: 6591 Cov.: 32 AF XY: 0.270 AC XY: 20080 AN XY: 74274

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.281

Alfa AF: 0.287 Hom.: 1027

Bravo AF: 0.264

Asia WGS AF: 0.249 AC: 863 AN: 3474

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	-0.87
CADD	Benign	4.7
DANN	Benign	0.59
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs10821136; hg19: chr9-96238731;