rs885048

Variant names:

• chr9-34399340-A-C
• rs885048
• NM_001184940.2:c.*1624T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-34399340-A-C
• chr9-34399340-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001184940.2(FAM219A):​c.*1624T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: FAM219A NM_001184940.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 9 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001184940.2. 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
	FAM219A	NM_001184940.2	MANE Select	c.*1624T>G		3_prime_UTR	Exon 6 of 6	NP_001171869.1
	FAM219A	NM_001184941.2		c.*1624T>G		3_prime_UTR	Exon 6 of 6	NP_001171870.1
	FAM219A	NM_001184942.2		c.*1624T>G		3_prime_UTR	Exon 6 of 6	NP_001171871.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM219A	ENST00000651358.1	MANE Select	c.*1624T>G		3_prime_UTR	Exon 6 of 6	ENSP00000499069.1
	FAM219A	ENST00000445726.5	TSL:2	c.*1624T>G		3_prime_UTR	Exon 6 of 6	ENSP00000392452.1
	FAM219A	ENST00000379089.5	TSL:3	c.*1624T>G		3_prime_UTR	Exon 6 of 6	ENSP00000368382.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 2650

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-0.16

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: rs885048; hg19: chr9-34399338;