rs10495305

Variant names:

• chr1-231236764-A-G
• rs10495305
• NM_152379.4:c.450+2093T>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.450+2093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 152,250 control chromosomes in the GnomAD database, including 763 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 0.061 (763 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: FSAF1 NM_152379.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSAF1	NM_152379.4	c.450+2093T>C		intron_variant	Intron 2 of 6	ENST00000366649.7	NP_689592.2
FSAF1	NM_001300830.2	c.450+2093T>C		intron_variant	Intron 2 of 6		NP_001287759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf131	ENST00000366649.7	c.450+2093T>C		intron_variant	Intron 2 of 6	1	NM_152379.4	ENSP00000355609.2

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9238 AN: 152132 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0241

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0522

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0609 AC: 9268 AN: 152250 Hom.: 763 Cov.: 32 AF XY: 0.0601 AC XY: 4478 AN XY: 74454

African (AFR) AF: 0.185 AC: 7697 AN: 41514

American (AMR) AF: 0.0241 AC: 369 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5190

South Asian (SAS) AF: 0.0106 AC: 51 AN: 4834

European-Finnish (FIN) AF: 0.0111 AC: 118 AN: 10622

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0120 AC: 815 AN: 68002

Other (OTH) AF: 0.0517 AC: 109 AN: 2110

Alfa AF: 0.0258 Hom.: 452

Bravo AF: 0.0667

Asia WGS AF: 0.0250 AC: 85 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	0.45
DANN	Benign	0.82
PhyloP100		-1.2
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: rs10495305; hg19: chr1-231372510;