4-89074274-G-A

Variant names:

• chr4-89074274-G-A
• rs6835031
• ENST00000502459.5:n.357+36768C>T

Variant summary

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

The ENST00000502459.5(FAM13A):​n.357+36768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,958 control chromosomes in the GnomAD database, including 42,074 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 0.74 (42074 hom., cov: 31)
• Consequence: FAM13A ENST00000502459.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13A	ENST00000502459.5	n.357+36768C>T		intron_variant	Intron 1 of 12	2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112858 AN: 151840 Hom.: 42043 Cov.: 31

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.743 AC: 112945 AN: 151958 Hom.: 42074 Cov.: 31 AF XY: 0.746 AC XY: 55422 AN XY: 74260

African (AFR) AF: 0.753 AC: 31190 AN: 41412

American (AMR) AF: 0.771 AC: 11774 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2482 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4224 AN: 5152

South Asian (SAS) AF: 0.821 AC: 3956 AN: 4820

European-Finnish (FIN) AF: 0.760 AC: 8032 AN: 10562

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48802 AN: 67962

Other (OTH) AF: 0.741 AC: 1561 AN: 2108

Alfa AF: 0.735 Hom.: 6886

Bravo AF: 0.742

Asia WGS AF: 0.801 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.43
PhyloP100		0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6835031; hg19: chr4-89995425;