rs4879787

Positions:

• chr9-34426660-G-C

Variant summary

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

The NM_001184940.2(FAM219A):​c.61-20696C>G variant causes a intron change. The variant allele was found at a frequency of 0.254 in 152,168 control chromosomes in the GnomAD database, including 5,105 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 0.25 (5105 hom., cov: 33)
• Consequence: FAM219A NM_001184940.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.56

Genes affected

FAM219A (HGNC:19920): (family with sequence similarity 219 member A) The protein encoded by this gene has homologs that have been identified in mouse, macaque, etc organisms. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM219A	NM_001184940.2	c.61-20696C>G		intron_variant		ENST00000651358.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM219A	ENST00000651358.1	c.61-20696C>G		intron_variant			NM_001184940.2	P3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38663 AN: 152048 Hom.: 5104 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.254 AC: 38698 AN: 152168 Hom.: 5105 Cov.: 33 AF XY: 0.259 AC XY: 19282 AN XY: 74372

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.235

Alfa AF: 0.245 Hom.: 577

Bravo AF: 0.245

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	20
DANN	Benign	0.61

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: rs4879787; hg19: chr9-34426658;