rs3822072

Positions:

• chr4-88820118-G-A
• chr4-88820118-G-C
• chr4-88820118-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.1008-15066C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,982 control chromosomes in the GnomAD database, including 18,761 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 0.49 (18761 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

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 (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM13A	NM_014883.4	c.1008-15066C>T		intron_variant		ENST00000264344.10	NP_055698.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM13A	ENST00000264344.10	c.1008-15066C>T		intron_variant		5	NM_014883.4	ENSP00000264344	P1

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74939 AN: 151864 Hom.: 18741 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.493 AC: 74996 AN: 151982 Hom.: 18761 Cov.: 32 AF XY: 0.498 AC XY: 36994 AN XY: 74252

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.482

Alfa AF: 0.354 Hom.: 968

Bravo AF: 0.486

Asia WGS AF: 0.580 AC: 2020 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.61

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: rs3822072; hg19: chr4-89741269;