chr4-89074274-G-A

Position:

• chr4-89074274-G-A

Variant summary

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

The ENST00000502459.5(FAM13A):​n.357+36768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,958 control chromosomes in the GnomAD database, including 42,074 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 0.74 (42074 hom., cov: 31)
• Consequence: FAM13A ENST00000502459.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM13A	ENST00000502459.5	n.357+36768C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112858 AN: 151840 Hom.: 42043 Cov.: 31

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.743 AC: 112945 AN: 151958 Hom.: 42074 Cov.: 31 AF XY: 0.746 AC XY: 55422 AN XY: 74260

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.741

Alfa AF: 0.735 Hom.: 6667

Bravo AF: 0.742

Asia WGS AF: 0.801 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6835031; hg19: chr4-89995425;