rs9374781

Positions:

• chr6-119123619-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• 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/exons	MANE	UniProt
FAM184A	NM_001100411.3	c.-202+25459C>T		intron_variant
FAM184A	NM_001288576.2	c.-202+25459C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM184A	ENST00000352896.9	c.-202+25459C>T		intron_variant		1
	ENST00000518570.2	n.457-56238G>A		intron_variant, non_coding_transcript_variant		2
FAM184A	ENST00000368475.8	c.-202+25459C>T		intron_variant		2
FAM184A	ENST00000475529.7	c.-202+25459C>T		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.502

Alfa AF: 0.521 Hom.: 9713

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9374781; hg19: chr6-119444784;