rs10516823

chr4-88876487-G-Achr4-88876487-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014883.4(FAM13A):c.844-25304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,034 control chromosomes in the GnomAD database, including 704 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 0.094 (704 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM13A	NM_014883.4	c.844-25304C>T		intron_variant		ENST00000264344.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM13A	ENST00000264344.10	c.844-25304C>T		intron_variant		5	NM_014883.4	P1

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14203 AN: 151916 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.0909

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0935 AC: 14221 AN: 152034 Hom.: 704 Cov.: 32 AF XY: 0.0942 AC XY: 7001 AN XY: 74308

Gnomad4 AFR AF: 0.0910

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0977

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.0955

Gnomad4 OTH AF: 0.0984

Alfa AF: 0.0915 Hom.: 848

Bravo AF: 0.0937

Asia WGS AF: 0.124 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.62
Dann	Benign	0.25

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: rs10516823; hg19: chr4-89797638;