6-119109061-T-C

Variant names:

• chr6-119109061-T-C
• rs9320678
• ENST00000352896.9:c.-202+40017A>G

Variant summary

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

The ENST00000352896.9(FAM184A):​c.-202+40017A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 150,174 control chromosomes in the GnomAD database, including 59,575 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 0.89 (59575 hom., cov: 30)
• Consequence: FAM184A ENST00000352896.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM184A	NM_001100411.3	c.-202+40017A>G		intron_variant	Intron 1 of 16		NP_001093881.1
FAM184A	NM_001288576.2	c.-202+40017A>G		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+40017A>G		intron_variant	Intron 1 of 16	1		ENSP00000326608.6
FAM184A	ENST00000368475.8	c.-202+40017A>G		intron_variant	Intron 1 of 15	2		ENSP00000357460.4
FAM184A	ENST00000475529.7	n.-202+40017A>G		intron_variant	Intron 1 of 18	5		ENSP00000429080.2

Frequencies

GnomAD3 genomes AF: 0.889 AC: 133428 AN: 150062 Hom.: 59527 Cov.: 30

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.889 AC: 133534 AN: 150174 Hom.: 59575 Cov.: 30 AF XY: 0.895 AC XY: 65703 AN XY: 73428

African (AFR) AF: 0.901 AC: 35695 AN: 39604

American (AMR) AF: 0.917 AC: 13979 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3052 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5168 AN: 5172

South Asian (SAS) AF: 0.932 AC: 4488 AN: 4814

European-Finnish (FIN) AF: 0.896 AC: 9462 AN: 10560

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58755 AN: 67996

Other (OTH) AF: 0.903 AC: 1900 AN: 2104

Alfa AF: 0.877 Hom.: 65666

Bravo AF: 0.894

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.45
PhyloP100		-1.6
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: rs9320678; hg19: chr6-119430226;