rs16854012

Variant names:

• chr1-231227254-A-G
• rs16854012
• NM_152379.4:c.511-186T>C

Variant summary

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

The NM_152379.4(FSAF1):​c.511-186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 152,106 control chromosomes in the GnomAD database, including 857 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 0.089 (857 hom., cov: 31)
• Consequence: FSAF1 NM_152379.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 4 publications found

Genes affected

FSAF1 (HGNC:25332): (chromosome 1 open reading frame 131) Enables RNA binding activity. Located in chromosome. [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 (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSAF1	NM_152379.4	c.511-186T>C		intron_variant	Intron 3 of 6	ENST00000366649.7	NP_689592.2
FSAF1	NM_001300830.2	c.508-186T>C		intron_variant	Intron 3 of 6		NP_001287759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf131	ENST00000366649.7	c.511-186T>C		intron_variant	Intron 3 of 6	1	NM_152379.4	ENSP00000355609.2

Frequencies

GnomAD3 genomes AF: 0.0887 AC: 13486 AN: 151988 Hom.: 858 Cov.: 31

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0747

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0862

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0886 AC: 13480 AN: 152106 Hom.: 857 Cov.: 31 AF XY: 0.0944 AC XY: 7018 AN XY: 74346

African (AFR) AF: 0.0213 AC: 883 AN: 41526

American (AMR) AF: 0.166 AC: 2539 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0747 AC: 259 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1614 AN: 5156

South Asian (SAS) AF: 0.154 AC: 741 AN: 4814

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10580

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0862 AC: 5860 AN: 67976

Other (OTH) AF: 0.0955 AC: 202 AN: 2116

Alfa AF: 0.0908 Hom.: 1507

Bravo AF: 0.0935

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		0.76
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: rs16854012; hg19: chr1-231363000; COSMIC: COSV107392214; COSMIC: COSV107392214;