rs9374781

Variant names:

• chr6-119123619-G-A
• rs9374781
• ENST00000352896.9:c.-202+25459C>T

Variant summary

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

The ENST00000352896.9(FAM184A):​c.-202+25459C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,932 control chromosomes in the GnomAD database, including 19,478 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 0.49 (19478 hom., cov: 31)
• Consequence: FAM184A ENST00000352896.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM184A	NM_001100411.3	c.-202+25459C>T		intron_variant	Intron 1 of 16		NP_001093881.1
FAM184A	NM_001288576.2	c.-202+25459C>T		intron_variant	Intron 1 of 15		NP_001275505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM184A	ENST00000352896.9	c.-202+25459C>T		intron_variant	Intron 1 of 16	1		ENSP00000326608.6
FAM184A	ENST00000368475.8	c.-202+25459C>T		intron_variant	Intron 1 of 15	2		ENSP00000357460.4
FAM184A	ENST00000475529.7	n.-202+25459C>T		intron_variant	Intron 1 of 18	5		ENSP00000429080.2

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74195 AN: 151814 Hom.: 19471 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.488 AC: 74211 AN: 151932 Hom.: 19478 Cov.: 31 AF XY: 0.496 AC XY: 36814 AN XY: 74278

African (AFR) AF: 0.296 AC: 12246 AN: 41424

American (AMR) AF: 0.631 AC: 9641 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1826 AN: 3466

East Asian (EAS) AF: 0.675 AC: 3478 AN: 5154

South Asian (SAS) AF: 0.620 AC: 2990 AN: 4820

European-Finnish (FIN) AF: 0.534 AC: 5630 AN: 10548

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36803 AN: 67946

Other (OTH) AF: 0.502 AC: 1056 AN: 2104

Alfa AF: 0.521 Hom.: 10916

Bravo AF: 0.490

Asia WGS AF: 0.588 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-2.0
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: rs9374781; hg19: chr6-119444784;