chr4-89021712-C-T

Variant names:

• chr4-89021712-C-T
• rs1795722
• NM_014883.4:c.218-1043G>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.218-1043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,096 control chromosomes in the GnomAD database, including 51,386 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 0.82 (51386 hom., cov: 30)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 5 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 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.218-1043G>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.218-1043G>A		intron	N/A	ENSP00000264344.5
	FAM13A	ENST00000511976.5	TSL:1	c.-232-1043G>A		intron	N/A	ENSP00000421914.1
	FAM13A	ENST00000509094.5	TSL:1	c.218-1043G>A		intron	N/A	ENSP00000426517.1

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124505 AN: 151978 Hom.: 51341 Cov.: 30

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.819 AC: 124600 AN: 152096 Hom.: 51386 Cov.: 30 AF XY: 0.819 AC XY: 60885 AN XY: 74352

African (AFR) AF: 0.904 AC: 37517 AN: 41500

American (AMR) AF: 0.745 AC: 11373 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3277 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3219 AN: 5162

South Asian (SAS) AF: 0.840 AC: 4047 AN: 4820

European-Finnish (FIN) AF: 0.812 AC: 8587 AN: 10578

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53822 AN: 67978

Other (OTH) AF: 0.821 AC: 1735 AN: 2112

Alfa AF: 0.810 Hom.: 36990

Bravo AF: 0.819

Asia WGS AF: 0.748 AC: 2606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.15
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: rs1795722; hg19: chr4-89942863;