chr4-88744042-A-G

Position:

• chr4-88744042-A-G

Variant summary

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

The NM_014883.4(FAM13A):​c.2466+2890T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,174 control chromosomes in the GnomAD database, including 2,924 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 0.17 (2924 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM13A	NM_014883.4	c.2466+2890T>C		intron_variant		ENST00000264344.10	NP_055698.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM13A	ENST00000264344.10	c.2466+2890T>C		intron_variant		5	NM_014883.4	ENSP00000264344	P1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26450 AN: 152056 Hom.: 2916 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.174 AC: 26480 AN: 152174 Hom.: 2924 Cov.: 32 AF XY: 0.178 AC XY: 13274 AN XY: 74396

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.0954

Gnomad4 ASJ AF: 0.0787

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.138

Alfa AF: 0.118 Hom.: 1800

Bravo AF: 0.171

Asia WGS AF: 0.334 AC: 1162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.79

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: rs3775391; hg19: chr4-89665193;