6-119136749-T-C

Variant names:

• chr6-119136749-T-C
• rs606955
• ENST00000352896.9:c.-202+12329A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001100411.3(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 NM_001100411.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001100411.3. 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_001100411.3		c.-202+12329A>G		intron	N/A	NP_001093881.1	Q8NB25-4
	FAM184A	NM_001288576.2		c.-202+12329A>G		intron	N/A	NP_001275505.1	H7BY63

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM184A	ENST00000352896.9	TSL:1	c.-202+12329A>G		intron	N/A	ENSP00000326608.6	Q8NB25-4
	FAM184A	ENST00000368475.8	TSL:2	c.-202+12329A>G		intron	N/A	ENSP00000357460.4	H7BY63
	FAM184A	ENST00000475529.7	TSL:5	n.-202+12329A>G		intron	N/A	ENSP00000429080.2	H0YBA5

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

African (AFR) AF: 0.907 AC: 37713 AN: 41564

American (AMR) AF: 0.727 AC: 11120 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3077 AN: 3468

East Asian (EAS) AF: 0.886 AC: 4591 AN: 5182

South Asian (SAS) AF: 0.915 AC: 4415 AN: 4824

European-Finnish (FIN) AF: 0.931 AC: 9894 AN: 10622

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58498 AN: 68008

Other (OTH) AF: 0.860 AC: 1817 AN: 2112

Alfa AF: 0.856 Hom.: 102937

Bravo AF: 0.852

Asia WGS AF: 0.886 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		0.047
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs606955; hg19: chr6-119457914;