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. Variant got -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

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM184A	NM_024581.6	c.2088+2513A>T		intron_variant	Intron 9 of 17	ENST00000338891.12	NP_078857.5
FAM184A	NM_001100411.3	c.1728+2513A>T		intron_variant	Intron 9 of 16		NP_001093881.1
FAM184A	NM_001288576.2	c.1728+2513A>T		intron_variant	Intron 9 of 15		NP_001275505.1
LOC124901389	XR_007059729.1	n.77-31019T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM184A	ENST00000338891.12	c.2088+2513A>T		intron_variant	Intron 9 of 17	1	NM_024581.6	ENSP00000342604.7

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 v4.3

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

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: rs10499090; hg19: chr6-119321551;