rs1964516

Positions:

• chr4-88954758-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014883.4(FAM13A):​c.606-16517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,516 control chromosomes in the GnomAD database, including 15,699 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 0.45 (15699 hom., cov: 29)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM13A	NM_014883.4	c.606-16517G>A		intron_variant		ENST00000264344.10
LOC105377327	XR_938977.3	n.2901-2637C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM13A	ENST00000264344.10	c.606-16517G>A		intron_variant		5	NM_014883.4	P1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68634 AN: 151402 Hom.: 15683 Cov.: 29

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.453 AC: 68667 AN: 151516 Hom.: 15699 Cov.: 29 AF XY: 0.452 AC XY: 33434 AN XY: 74008

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.430

Alfa AF: 0.479 Hom.: 2187

Bravo AF: 0.444

Asia WGS AF: 0.481 AC: 1674 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	1.4
DANN	Benign	0.48

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: rs1964516; hg19: chr4-89875909;