rs3775391

Variant names:

• chr4-88744042-A-G
• rs3775391
• NM_014883.4:c.2466+2890T>C

Variant summary

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

The NM_014883.4(FAM13A):​c.2466+2890T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,174 control chromosomes in the GnomAD database, including 2,924 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 0.17 (2924 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014883.4. 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
	FAM13A	NM_014883.4	MANE Select	c.2466+2890T>C		intron	N/A	NP_055698.2
	FAM13A	NM_001015045.3		c.1488+2890T>C		intron	N/A	NP_001015045.1
	FAM13A	NM_001265578.2		c.1446+2890T>C		intron	N/A	NP_001252507.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	ENST00000264344.10	TSL:5 MANE Select	c.2466+2890T>C		intron	N/A	ENSP00000264344.5
	FAM13A	ENST00000503556.5	TSL:1	c.1446+2890T>C		intron	N/A	ENSP00000427189.1
	FAM13A	ENST00000395002.6	TSL:1	c.1488+2890T>C		intron	N/A	ENSP00000378450.2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26450 AN: 152056 Hom.: 2916 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.174 AC: 26480 AN: 152174 Hom.: 2924 Cov.: 32 AF XY: 0.178 AC XY: 13274 AN XY: 74396

African (AFR) AF: 0.290 AC: 12034 AN: 41490

American (AMR) AF: 0.0954 AC: 1461 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1566 AN: 5162

South Asian (SAS) AF: 0.323 AC: 1553 AN: 4814

European-Finnish (FIN) AF: 0.175 AC: 1856 AN: 10604

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7346 AN: 68014

Other (OTH) AF: 0.138 AC: 292 AN: 2110

Alfa AF: 0.122 Hom.: 2441

Bravo AF: 0.171

Asia WGS AF: 0.334 AC: 1162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.79
PhyloP100		0.24
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: rs3775391; hg19: chr4-89665193;