rs13088795

Variant names:

• chr3-58576798-C-T
• rs13088795
• NM_001076778.3:c.-6+511G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001076778.3(FAM107A):​c.-6+511G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,244 control chromosomes in the GnomAD database, including 1,584 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 (1584 hom., cov: 33)
• Consequence: FAM107A NM_001076778.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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.-6+511G>A		intron	N/A	NP_001070246.1
	FAM107A	NM_001282714.2		c.89-6933G>A		intron	N/A	NP_001269643.1
	FAM107A	NM_001282713.2		c.80-6933G>A		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.-6+511G>A		intron	N/A	ENSP00000354270.2
	FAM107A	ENST00000447756.2	TSL:1	c.80-6933G>A		intron	N/A	ENSP00000400858.2
	FAM107A	ENST00000394481.5	TSL:1	c.-104+511G>A		intron	N/A	ENSP00000377991.1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20867 AN: 152126 Hom.: 1577 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.137 AC: 20898 AN: 152244 Hom.: 1584 Cov.: 33 AF XY: 0.137 AC XY: 10172 AN XY: 74422

African (AFR) AF: 0.139 AC: 5780 AN: 41560

American (AMR) AF: 0.110 AC: 1679 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.0581 AC: 280 AN: 4822

European-Finnish (FIN) AF: 0.214 AC: 2261 AN: 10566

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9982 AN: 68022

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.138 Hom.: 2729

Bravo AF: 0.130

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.58
PhyloP100		0.077
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: rs13088795; hg19: chr3-58562525;