rs10499090

Variant names:

• chr6-119000386-T-A
• rs10499090
• NM_024581.6:c.2088+2513A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-119000386-T-A
• chr6-119000386-T-C
• chr6-119000386-T-G

Variant summary

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

The NM_024581.6(FAM184A):​c.2088+2513A>T variant causes a intron 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: FAM184A NM_024581.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74
• Publications: 3 publications found

Genes affected

FAM184A (HGNC:20991): (family with sequence similarity 184 member A) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000253194 (HGNC:):

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=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024581.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM184A	NM_024581.6	MANE Select	c.2088+2513A>T		intron	N/A	NP_078857.5
	FAM184A	NM_001100411.3		c.1728+2513A>T		intron	N/A	NP_001093881.1	Q8NB25-4
	FAM184A	NM_001288576.2		c.1728+2513A>T		intron	N/A	NP_001275505.1	H7BY63

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM184A	ENST00000338891.12	TSL:1 MANE Select	c.2088+2513A>T		intron	N/A	ENSP00000342604.7	Q8NB25-1
	FAM184A	ENST00000352896.9	TSL:1	c.1728+2513A>T		intron	N/A	ENSP00000326608.6	Q8NB25-4
	FAM184A	ENST00000621231.4	TSL:5	c.1962+2513A>T		intron	N/A	ENSP00000484827.1	A0A087X2A7

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		-2.7

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: rs10499090; hg19: chr6-119321551;