4-88821613-C-T

Variant names:

• chr4-88821613-C-T
• rs2869950
• NM_014883.4:c.1008-16561G>A

Variant summary

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

The NM_014883.4(FAM13A):​c.1008-16561G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,904 control chromosomes in the GnomAD database, including 14,060 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 0.43 (14060 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.632 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	NM_014883.4	MANE Select	c.1008-16561G>A		intron	N/A	NP_055698.2	O94988-4
	FAM13A	NM_001015045.3		c.29+1363G>A		intron	N/A	NP_001015045.1	O94988-1
	FAM13A	NM_001265578.2		c.29+1363G>A		intron	N/A	NP_001252507.1	O94988-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	ENST00000264344.10	TSL:5 MANE Select	c.1008-16561G>A		intron	N/A	ENSP00000264344.5	O94988-4
	FAM13A	ENST00000503556.5	TSL:1	c.29+1363G>A		intron	N/A	ENSP00000427189.1	O94988-5
	FAM13A	ENST00000395002.6	TSL:1	c.29+1363G>A		intron	N/A	ENSP00000378450.2	O94988-3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64608 AN: 151786 Hom.: 14056 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.426 AC: 64644 AN: 151904 Hom.: 14060 Cov.: 32 AF XY: 0.430 AC XY: 31933 AN XY: 74254

African (AFR) AF: 0.435 AC: 17992 AN: 41400

American (AMR) AF: 0.405 AC: 6186 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3352 AN: 5156

South Asian (SAS) AF: 0.519 AC: 2501 AN: 4822

European-Finnish (FIN) AF: 0.419 AC: 4412 AN: 10534

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.399 AC: 27113 AN: 67950

Other (OTH) AF: 0.433 AC: 915 AN: 2112

Alfa AF: 0.408 Hom.: 54870

Bravo AF: 0.424

Asia WGS AF: 0.522 AC: 1817 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.49
PhyloP100		0.18
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: rs2869950; hg19: chr4-89742764;