rs1334927

Variant names:

• chr6-119074043-T-C
• rs1334927
• NM_024581.6:c.159+4098A>G

Variant summary

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

The NM_024581.6(FAM184A):​c.159+4098A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 152,214 control chromosomes in the GnomAD database, including 699 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 0.065 (699 hom., cov: 32)
• Consequence: FAM184A NM_024581.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

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.159+4098A>G		intron	N/A	NP_078857.5
	FAM184A	NM_001100411.3		c.-201-49230A>G		intron	N/A	NP_001093881.1	Q8NB25-4
	FAM184A	NM_001288576.2		c.-201-49230A>G		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.159+4098A>G		intron	N/A	ENSP00000342604.7	Q8NB25-1
	FAM184A	ENST00000352896.9	TSL:1	c.-201-49230A>G		intron	N/A	ENSP00000326608.6	Q8NB25-4
	FAM184A	ENST00000522284.5	TSL:1	c.-202+4962A>G		intron	N/A	ENSP00000429826.1	E7EQ67

Frequencies

GnomAD3 genomes AF: 0.0646 AC: 9823 AN: 152098 Hom.: 697 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0646 AC: 9829 AN: 152214 Hom.: 699 Cov.: 32 AF XY: 0.0637 AC XY: 4742 AN XY: 74408

African (AFR) AF: 0.176 AC: 7287 AN: 41494

American (AMR) AF: 0.0271 AC: 414 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.00684 AC: 33 AN: 4828

European-Finnish (FIN) AF: 0.0457 AC: 485 AN: 10610

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0216 AC: 1469 AN: 68026

Other (OTH) AF: 0.0468 AC: 99 AN: 2114

Alfa AF: 0.0630 Hom.: 83

Bravo AF: 0.0674

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1334927; hg19: chr6-119395208;