4-88947927-C-T

Variant names:

• chr4-88947927-C-T
• rs2869966
• NM_014883.4:c.606-9686G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014883.4(FAM13A):​c.606-9686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,858 control chromosomes in the GnomAD database, including 16,893 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 0.46 (16893 hom., cov: 31)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 24 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13A	NM_014883.4	c.606-9686G>A		intron_variant	Intron 4 of 23	ENST00000264344.10	NP_055698.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13A	ENST00000264344.10	c.606-9686G>A		intron_variant	Intron 4 of 23	5	NM_014883.4	ENSP00000264344.5

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70408 AN: 151740 Hom.: 16854 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.464 AC: 70495 AN: 151858 Hom.: 16893 Cov.: 31 AF XY: 0.462 AC XY: 34279 AN XY: 74184

African (AFR) AF: 0.598 AC: 24765 AN: 41380

American (AMR) AF: 0.451 AC: 6876 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3466

East Asian (EAS) AF: 0.517 AC: 2672 AN: 5170

South Asian (SAS) AF: 0.356 AC: 1713 AN: 4808

European-Finnish (FIN) AF: 0.431 AC: 4521 AN: 10496

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27599 AN: 67984

Other (OTH) AF: 0.432 AC: 912 AN: 2110

Alfa AF: 0.417 Hom.: 54420

Bravo AF: 0.471

Asia WGS AF: 0.451 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.75
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2869966; hg19: chr4-89869078;