4-88855930-A-G

Variant names:

• chr4-88855930-A-G
• rs6830970
• NM_014883.4:c.844-4747T>C

Variant summary

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

The NM_014883.4(FAM13A):​c.844-4747T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,988 control chromosomes in the GnomAD database, including 11,234 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 0.38 (11234 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 20 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]

LOC124900732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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.844-4747T>C		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.844-4747T>C		intron	N/A	ENSP00000264344.5
	FAM13A	ENST00000511976.5	TSL:1	c.216+50449T>C		intron	N/A	ENSP00000421914.1
	FAM13A	ENST00000511145.1	TSL:3	n.323T>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57737 AN: 151870 Hom.: 11202 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.360

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.380 AC: 57804 AN: 151988 Hom.: 11234 Cov.: 32 AF XY: 0.381 AC XY: 28313 AN XY: 74284

African (AFR) AF: 0.408 AC: 16904 AN: 41450

American (AMR) AF: 0.456 AC: 6961 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2598 AN: 5142

South Asian (SAS) AF: 0.270 AC: 1298 AN: 4814

European-Finnish (FIN) AF: 0.360 AC: 3799 AN: 10552

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24150 AN: 67964

Other (OTH) AF: 0.368 AC: 778 AN: 2116

Alfa AF: 0.357 Hom.: 42697

Bravo AF: 0.391

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.95
DANN	Benign	0.59
PhyloP100		-0.14
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: rs6830970; hg19: chr4-89777081; COSMIC: COSV107262832;