rs1964516

Variant names:

• chr4-88954758-C-T
• rs1964516
• NM_014883.4:c.606-16517G>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.606-16517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,516 control chromosomes in the GnomAD database, including 15,699 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 0.45 (15699 hom., cov: 29)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 25 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]

LOC105377327 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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.606-16517G>A		intron	N/A	NP_055698.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	ENST00000264344.10	TSL:5 MANE Select	c.606-16517G>A		intron	N/A	ENSP00000264344.5
	FAM13A	ENST00000511976.5	TSL:1	c.-22-16517G>A		intron	N/A	ENSP00000421914.1
	FAM13A	ENST00000509094.5	TSL:1	c.606-16517G>A		intron	N/A	ENSP00000426517.1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68634 AN: 151402 Hom.: 15683 Cov.: 29

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.453 AC: 68667 AN: 151516 Hom.: 15699 Cov.: 29 AF XY: 0.452 AC XY: 33434 AN XY: 74008

African (AFR) AF: 0.355 AC: 14664 AN: 41250

American (AMR) AF: 0.468 AC: 7121 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3464

East Asian (EAS) AF: 0.526 AC: 2702 AN: 5136

South Asian (SAS) AF: 0.443 AC: 2128 AN: 4804

European-Finnish (FIN) AF: 0.497 AC: 5192 AN: 10450

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34141 AN: 67898

Other (OTH) AF: 0.430 AC: 905 AN: 2104

Alfa AF: 0.479 Hom.: 2187

Bravo AF: 0.444

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.93
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: rs1964516; hg19: chr4-89875909;