12-132512822-T-C

Position:

• chr12-132512822-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367871.1(FBRSL1):​c.489+4472T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,236 control chromosomes in the GnomAD database, including 61,279 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 0.89 (61279 hom., cov: 34)
• Consequence: FBRSL1 NM_001367871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

FBRSL1 (HGNC:29308): (fibrosin like 1) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBRSL1	NM_001367871.1	c.489+4472T>C		intron_variant		ENST00000680143.1	NP_001354800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBRSL1	ENST00000680143.1	c.489+4472T>C		intron_variant			NM_001367871.1	ENSP00000505341	A2
FBRSL1	ENST00000434748.2	c.489+4472T>C		intron_variant		1		ENSP00000396160	P2
FBRSL1	ENST00000650108.1	c.489+4472T>C		intron_variant				ENSP00000496901	A2

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135258 AN: 152118 Hom.: 61249 Cov.: 34

Gnomad AFR AF: 0.750

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.889 AC: 135341 AN: 152236 Hom.: 61279 Cov.: 34 AF XY: 0.885 AC XY: 65882 AN XY: 74430

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.912

Alfa AF: 0.934 Hom.: 8317

Bravo AF: 0.874

Asia WGS AF: 0.815 AC: 2834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.50
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.1

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: rs2323991; hg19: chr12-133089408;