4-88962828-C-T

Position:

• chr4-88962828-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014883.4(FAM13A):​c.606-24587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,860 control chromosomes in the GnomAD database, including 20,944 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.52 (20944 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1 O:1
• Conservation: PhyloP100: -0.901

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 4-88962828-C-T is Benign according to our data. Variant chr4-88962828-C-T is described in ClinVar as [Benign]. Clinvar id is 1027618.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM13A	NM_014883.4	c.606-24587G>A		intron_variant		ENST00000264344.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM13A	ENST00000264344.10	c.606-24587G>A		intron_variant		5	NM_014883.4	P1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79664 AN: 151744 Hom.: 20921 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.525 AC: 79725 AN: 151860 Hom.: 20944 Cov.: 32 AF XY: 0.521 AC XY: 38682 AN XY: 74210

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.490

Alfa AF: 0.485 Hom.: 40909

Bravo AF: 0.527

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 17, 2020

This variant is associated with the following publications: (PMID: 30079747) -

Chronic obstructive pulmonary disease Other:1

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Feb 03, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.16
DANN	Benign	0.57

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: rs7671167; hg19: chr4-89883979;