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GeneBe

rs958998

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032448.3(FAM120B):c.2284-350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,152 control chromosomes in the GnomAD database, including 47,616 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 0.79 ( 47616 hom., cov: 32)

Consequence

FAM120B
NM_032448.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.111
Variant links:
Genes affected
FAM120B (HGNC:21109): (family with sequence similarity 120 member B) Predicted to be involved in fat cell differentiation and peroxisome proliferator activated receptor signaling pathway. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FAM120BNM_032448.3 linkuse as main transcriptc.2284-350A>G intron_variant ENST00000476287.4
LOC124901474XR_007059897.1 linkuse as main transcriptn.137-358T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FAM120BENST00000476287.4 linkuse as main transcriptc.2284-350A>G intron_variant 1 NM_032448.3 A2Q96EK7-1
FAM120BENST00000537664.5 linkuse as main transcriptc.2353-350A>G intron_variant 2 A2
FAM120BENST00000625626.1 linkuse as main transcriptc.280-350A>G intron_variant 2 P2Q96EK7-3
FAM120BENST00000630384.2 linkuse as main transcriptc.2320-350A>G intron_variant 2 A2

Frequencies

GnomAD3 genomes
AF:
0.790
AC:
120114
AN:
152034
Hom.:
47582
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.790
Gnomad AMI
AF:
0.603
Gnomad AMR
AF:
0.818
Gnomad ASJ
AF:
0.778
Gnomad EAS
AF:
0.942
Gnomad SAS
AF:
0.884
Gnomad FIN
AF:
0.757
Gnomad MID
AF:
0.744
Gnomad NFE
AF:
0.775
Gnomad OTH
AF:
0.781
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.790
AC:
120205
AN:
152152
Hom.:
47616
Cov.:
32
AF XY:
0.793
AC XY:
58989
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.789
Gnomad4 AMR
AF:
0.818
Gnomad4 ASJ
AF:
0.778
Gnomad4 EAS
AF:
0.942
Gnomad4 SAS
AF:
0.883
Gnomad4 FIN
AF:
0.757
Gnomad4 NFE
AF:
0.775
Gnomad4 OTH
AF:
0.781
Alfa
AF:
0.779
Hom.:
93559
Bravo
AF:
0.792
Asia WGS
AF:
0.920
AC:
3199
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
0.88
Dann
Benign
0.47

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs958998; hg19: chr6-170697025; API