rs910424

Variant summary

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

The NM_032448.3(FAM120B):​c.2190+545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,082 control chromosomes in the GnomAD database, including 5,496 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 0.24 ( 5496 hom., cov: 32)

Consequence

FAM120B
NM_032448.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAM120BNM_032448.3 linkuse as main transcriptc.2190+545G>A intron_variant ENST00000476287.4 NP_115824.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM120BENST00000476287.4 linkuse as main transcriptc.2190+545G>A intron_variant 1 NM_032448.3 ENSP00000417970 A2Q96EK7-1
FAM120BENST00000537664.5 linkuse as main transcriptc.2259+545G>A intron_variant 2 ENSP00000440125 A2
FAM120BENST00000625626.1 linkuse as main transcriptc.186+545G>A intron_variant 2 ENSP00000485793 P2Q96EK7-3
FAM120BENST00000630384.2 linkuse as main transcriptc.2226+545G>A intron_variant 2 ENSP00000485745 A2

Frequencies

GnomAD3 genomes
AF:
0.240
AC:
36509
AN:
151964
Hom.:
5488
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0810
Gnomad AMI
AF:
0.198
Gnomad AMR
AF:
0.326
Gnomad ASJ
AF:
0.358
Gnomad EAS
AF:
0.00770
Gnomad SAS
AF:
0.351
Gnomad FIN
AF:
0.267
Gnomad MID
AF:
0.358
Gnomad NFE
AF:
0.317
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.240
AC:
36512
AN:
152082
Hom.:
5496
Cov.:
32
AF XY:
0.242
AC XY:
17998
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0809
Gnomad4 AMR
AF:
0.325
Gnomad4 ASJ
AF:
0.358
Gnomad4 EAS
AF:
0.00791
Gnomad4 SAS
AF:
0.354
Gnomad4 FIN
AF:
0.267
Gnomad4 NFE
AF:
0.317
Gnomad4 OTH
AF:
0.252
Alfa
AF:
0.306
Hom.:
10347
Bravo
AF:
0.233
Asia WGS
AF:
0.161
AC:
562
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.4
DANN
Benign
0.41

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: rs910424; hg19: chr6-170657956; COSMIC: COSV53002456; API