3-58570168-T-C

Position:

• chr3-58570168-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.-5-303A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,254 control chromosomes in the GnomAD database, including 2,096 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 0.13 (2096 hom., cov: 32)
• Consequence: FAM107A NM_001076778.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM107A	NM_001076778.3	c.-5-303A>G		intron_variant		ENST00000360997.7	NP_001070246.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM107A	ENST00000360997.7	c.-5-303A>G		intron_variant		1	NM_001076778.3	ENSP00000354270.2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19249 AN: 152136 Hom.: 2093 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0724

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.127 AC: 19277 AN: 152254 Hom.: 2096 Cov.: 32 AF XY: 0.124 AC XY: 9201 AN XY: 74458

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0588

Gnomad4 NFE AF: 0.0724

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0956 Hom.: 523

Bravo AF: 0.134

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.61

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: rs9813011; hg19: chr3-58555895;