rs13315591

chr3-58571114-T-C

Variant summary

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

The NM_001076778.3(FAM107A):c.-5-1249A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,198 control chromosomes in the GnomAD database, including 2,775 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 0.14 (2775 hom., cov: 33)
• Consequence: FAM107A NM_001076778.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

Genes affected

FAM107A (HGNC:30827): (family with sequence similarity 107 member A) Predicted to enable actin binding activity. Involved in several processes, including negative regulation of G1/S transition of mitotic cell cycle; negative regulation of focal adhesion assembly; and regulation of cytoskeleton organization. Located in several cellular components, including focal adhesion; ruffle membrane; and stress fiber. [provided by Alliance of Genome Resources, Apr 2022]

LOC107984079 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM107A	NM_001076778.3	c.-5-1249A>G		intron_variant		ENST00000360997.7
LOC107984079	XR_001740724.2	n.944-1633T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM107A	ENST00000360997.7	c.-5-1249A>G		intron_variant		1	NM_001076778.3	A1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21490 AN: 152080 Hom.: 2770 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0589

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.141 AC: 21525 AN: 152198 Hom.: 2775 Cov.: 33 AF XY: 0.138 AC XY: 10300 AN XY: 74422

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.0712

Gnomad4 ASJ AF: 0.0554

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0292

Gnomad4 FIN AF: 0.0589

Gnomad4 NFE AF: 0.0732

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0781 Hom.: 900

Bravo AF: 0.151

Asia WGS AF: 0.0340 AC: 117 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	1.3
Dann	Benign	0.67

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: rs13315591; hg19: chr3-58556841;