6-119136749-T-C

Variant summary

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

The ENST00000352896.9(FAM184A):c.-202+12329A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,278 control chromosomes in the GnomAD database, including 57,609 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 0.87 (57609 hom., cov: 33)
• Consequence: FAM184A ENST00000352896.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM184A	NM_001100411.3	c.-202+12329A>G		intron_variant
FAM184A	NM_001288576.2	c.-202+12329A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM184A	ENST00000352896.9	c.-202+12329A>G		intron_variant		1
	ENST00000518570.2	n.457-43108T>C		intron_variant, non_coding_transcript_variant		2
FAM184A	ENST00000368475.8	c.-202+12329A>G		intron_variant		2
FAM184A	ENST00000475529.7	c.-202+12329A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.868 AC: 132071 AN: 152158 Hom.: 57570 Cov.: 33

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.868 AC: 132164 AN: 152278 Hom.: 57609 Cov.: 33 AF XY: 0.869 AC XY: 64736 AN XY: 74472

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.860

Alfa AF: 0.857 Hom.: 74253

Bravo AF: 0.852

Asia WGS AF: 0.886 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.4
Dann	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs606955; hg19: chr6-119457914;