rs9307055

Variant names:

• chr4-88979101-T-C
• rs9307055
• NM_014883.4:c.605+11872A>G

Variant summary

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

The NM_014883.4(FAM13A):​c.605+11872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,106 control chromosomes in the GnomAD database, including 38,981 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 0.71 (38981 hom., cov: 33)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65
• Publications: 2 publications found

Genes affected

FAM13A (HGNC:19367): (family with sequence similarity 13 member A) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. Implicated in chronic obstructive pulmonary disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13A	NM_014883.4	c.605+11872A>G		intron_variant	Intron 4 of 23	ENST00000264344.10	NP_055698.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13A	ENST00000264344.10	c.605+11872A>G		intron_variant	Intron 4 of 23	5	NM_014883.4	ENSP00000264344.5

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108340 AN: 151988 Hom.: 38936 Cov.: 33

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.713 AC: 108435 AN: 152106 Hom.: 38981 Cov.: 33 AF XY: 0.714 AC XY: 53072 AN XY: 74360

African (AFR) AF: 0.818 AC: 33944 AN: 41512

American (AMR) AF: 0.670 AC: 10245 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2875 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3183 AN: 5168

South Asian (SAS) AF: 0.670 AC: 3229 AN: 4822

European-Finnish (FIN) AF: 0.698 AC: 7359 AN: 10536

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45152 AN: 67984

Other (OTH) AF: 0.724 AC: 1530 AN: 2114

Alfa AF: 0.692 Hom.: 4727

Bravo AF: 0.717

Asia WGS AF: 0.644 AC: 2241 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.029
DANN	Benign	0.32
PhyloP100		-2.6
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: rs9307055; hg19: chr4-89900252;