3-58570168-T-C

Variant names:

• chr3-58570168-T-C
• rs9813011
• NM_001076778.3:c.-5-303A>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.-5-303A>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
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107A	NM_001076778.3	MANE Select	c.-5-303A>G		intron	N/A	NP_001070246.1	O95990-1
	FAM107A	NM_001282714.2		c.89-303A>G		intron	N/A	NP_001269643.1	O95990-4
	FAM107A	NM_001282713.2		c.80-303A>G		intron	N/A	NP_001269642.1	O95990-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107A	ENST00000360997.7	TSL:1 MANE Select	c.-5-303A>G		intron	N/A	ENSP00000354270.2	O95990-1
	FAM107A	ENST00000447756.2	TSL:1	c.80-303A>G		intron	N/A	ENSP00000400858.2	O95990-3
	FAM107A	ENST00000394481.5	TSL:1	c.-6+158A>G		intron	N/A	ENSP00000377991.1	O95990-1

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

African (AFR) AF: 0.292 AC: 12141 AN: 41510

American (AMR) AF: 0.0648 AC: 991 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4826

European-Finnish (FIN) AF: 0.0588 AC: 624 AN: 10620

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0724 AC: 4925 AN: 68016

Other (OTH) AF: 0.109 AC: 231 AN: 2116

Alfa AF: 0.0871 Hom.: 728

Bravo AF: 0.134

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.61
PhyloP100		0.45
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: rs9813011; hg19: chr3-58555895;