rs4416442

Variant names:

• chr4-88945562-T-C
• rs4416442
• NM_014883.4:c.606-7321A>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.606-7321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,328 control chromosomes in the GnomAD database, including 15,347 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 (15347 hom., cov: 29)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 22 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 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.606-7321A>G		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.606-7321A>G		intron	N/A	ENSP00000264344.5
	FAM13A	ENST00000511976.5	TSL:1	c.-22-7321A>G		intron	N/A	ENSP00000421914.1
	FAM13A	ENST00000509094.5	TSL:1	c.606-7321A>G		intron	N/A	ENSP00000426517.1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67516 AN: 151212 Hom.: 15322 Cov.: 29

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.447 AC: 67580 AN: 151328 Hom.: 15347 Cov.: 29 AF XY: 0.445 AC XY: 32881 AN XY: 73906

African (AFR) AF: 0.538 AC: 22114 AN: 41092

American (AMR) AF: 0.445 AC: 6762 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1024 AN: 3464

East Asian (EAS) AF: 0.517 AC: 2654 AN: 5136

South Asian (SAS) AF: 0.357 AC: 1715 AN: 4804

European-Finnish (FIN) AF: 0.429 AC: 4486 AN: 10464

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27548 AN: 67888

Other (OTH) AF: 0.417 AC: 873 AN: 2094

Alfa AF: 0.422 Hom.: 21132

Bravo AF: 0.452

Asia WGS AF: 0.442 AC: 1538 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.70
DANN	Benign	0.49
PhyloP100		-0.66
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: rs4416442; hg19: chr4-89866713;