rs4416442

Positions:

• chr4-88945562-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM13A	NM_014883.4	c.606-7321A>G		intron_variant		ENST00000264344.10
LOC105377327	XR_938977.3	n.2900+117T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM13A	ENST00000264344.10	c.606-7321A>G		intron_variant		5	NM_014883.4	P1

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

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.417

Alfa AF: 0.448 Hom.: 2160

Bravo AF: 0.452

Asia WGS AF: 0.442 AC: 1538 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.70
DANN	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs4416442; hg19: chr4-89866713;