3-58571114-T-C

Variant names:

• chr3-58571114-T-C
• rs13315591
• NM_001076778.3:c.-5-1249A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 44 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001076778.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107A	NM_001076778.3	MANE Select	c.-5-1249A>G		intron	N/A	NP_001070246.1
	FAM107A	NM_001282714.2		c.89-1249A>G		intron	N/A	NP_001269643.1
	FAM107A	NM_001282713.2		c.80-1249A>G		intron	N/A	NP_001269642.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107A	ENST00000360997.7	TSL:1 MANE Select	c.-5-1249A>G		intron	N/A	ENSP00000354270.2
	FAM107A	ENST00000447756.2	TSL:1	c.80-1249A>G		intron	N/A	ENSP00000400858.2
	FAM107A	ENST00000394481.5	TSL:1	c.-103-691A>G		intron	N/A	ENSP00000377991.1

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

African (AFR) AF: 0.343 AC: 14220 AN: 41490

American (AMR) AF: 0.0712 AC: 1090 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0554 AC: 192 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4824

European-Finnish (FIN) AF: 0.0589 AC: 625 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0732 AC: 4978 AN: 68014

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.0898 Hom.: 3450

Bravo AF: 0.151

Asia WGS AF: 0.0340 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-0.48
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: rs13315591; hg19: chr3-58556841;