chr6-170348868-G-A

Variant names:

• chr6-170348868-G-A
• rs910424
• NM_032448.3:c.2190+545G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.2190+545G>A		intron_variant	Intron 5 of 10	ENST00000476287.4	NP_115824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.2190+545G>A		intron_variant	Intron 5 of 10	1	NM_032448.3	ENSP00000417970.1
FAM120B	ENST00000537664.5	c.2259+545G>A		intron_variant	Intron 5 of 10	2		ENSP00000440125.1
FAM120B	ENST00000630384.2	c.2226+545G>A		intron_variant	Intron 5 of 10	2		ENSP00000485745.1
FAM120B	ENST00000625626.1	c.186+545G>A		intron_variant	Intron 3 of 8	2		ENSP00000485793.1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36509 AN: 151964 Hom.: 5488 Cov.: 32

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

African (AFR) AF: 0.0809 AC: 3355 AN: 41492

American (AMR) AF: 0.325 AC: 4968 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3470

East Asian (EAS) AF: 0.00791 AC: 41 AN: 5182

South Asian (SAS) AF: 0.354 AC: 1708 AN: 4824

European-Finnish (FIN) AF: 0.267 AC: 2815 AN: 10548

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21566 AN: 67962

Other (OTH) AF: 0.252 AC: 531 AN: 2110

Alfa AF: 0.292 Hom.: 21550

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
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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