chr4-88949813-C-T

Variant names:

• chr4-88949813-C-T
• rs2045517
• NM_014883.4:c.606-11572G>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.606-11572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,932 control chromosomes in the GnomAD database, including 18,652 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 0.48 (18652 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 27 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014883.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	NM_014883.4	MANE Select	c.606-11572G>A		intron	N/A	NP_055698.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	ENST00000264344.10	TSL:5 MANE Select	c.606-11572G>A		intron	N/A	ENSP00000264344.5
	FAM13A	ENST00000511976.5	TSL:1	c.-22-11572G>A		intron	N/A	ENSP00000421914.1
	FAM13A	ENST00000509094.5	TSL:1	c.606-11572G>A		intron	N/A	ENSP00000426517.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73288 AN: 151814 Hom.: 18609 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.483 AC: 73383 AN: 151932 Hom.: 18652 Cov.: 32 AF XY: 0.481 AC XY: 35678 AN XY: 74242

African (AFR) AF: 0.662 AC: 27399 AN: 41402

American (AMR) AF: 0.463 AC: 7068 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1039 AN: 3468

East Asian (EAS) AF: 0.516 AC: 2662 AN: 5158

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4552 AN: 10548

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27599 AN: 67940

Other (OTH) AF: 0.445 AC: 939 AN: 2108

Alfa AF: 0.461 Hom.: 4143

Bravo AF: 0.493

Asia WGS AF: 0.456 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.61
PhyloP100		-0.18
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: rs2045517; hg19: chr4-89870964;