rs17816002

Variant names:

• chr4-88877803-C-A
• rs17816002
• NM_014883.4:c.844-26620G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-88877803-C-A
• chr4-88877803-C-G
• chr4-88877803-C-T

Variant summary

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

The NM_014883.4(FAM13A):​c.844-26620G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,070 control chromosomes in the GnomAD database, including 6,082 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 0.27 (6082 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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.844-26620G>T		intron	N/A	NP_055698.2	O94988-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	ENST00000264344.10	TSL:5 MANE Select	c.844-26620G>T		intron	N/A	ENSP00000264344.5	O94988-4
	FAM13A	ENST00000511976.5	TSL:1	c.216+28576G>T		intron	N/A	ENSP00000421914.1	E9PGM7
	FAM13A	ENST00000933309.1		c.844-26620G>T		intron	N/A	ENSP00000603368.1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41087 AN: 151952 Hom.: 6081 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.270 AC: 41093 AN: 152070 Hom.: 6082 Cov.: 32 AF XY: 0.265 AC XY: 19694 AN XY: 74312

African (AFR) AF: 0.163 AC: 6773 AN: 41480

American (AMR) AF: 0.282 AC: 4310 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3464

East Asian (EAS) AF: 0.150 AC: 777 AN: 5172

South Asian (SAS) AF: 0.188 AC: 908 AN: 4822

European-Finnish (FIN) AF: 0.252 AC: 2662 AN: 10558

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22841 AN: 67984

Other (OTH) AF: 0.316 AC: 667 AN: 2112

Alfa AF: 0.316 Hom.: 23462

Bravo AF: 0.268

Asia WGS AF: 0.172 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.84
DANN	Benign	0.61
PhyloP100		-0.58
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: rs17816002; hg19: chr4-89798954; COSMIC: COSV52008935;