rs3756939

Positions:

• chr6-119019716-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024581.6(FAM184A):​c.1332+262A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,106 control chromosomes in the GnomAD database, including 25,218 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 0.56 (25218 hom., cov: 33)
• Consequence: FAM184A NM_024581.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM184A	NM_024581.6	c.1332+262A>G		intron_variant		ENST00000338891.12	NP_078857.5
LOC124901389	XR_007059729.1	n.77-11689T>C		intron_variant, non_coding_transcript_variant
FAM184A	NM_001100411.3	c.972+262A>G		intron_variant			NP_001093881.1
FAM184A	NM_001288576.2	c.972+262A>G		intron_variant			NP_001275505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM184A	ENST00000338891.12	c.1332+262A>G		intron_variant		1	NM_024581.6	ENSP00000342604	P1
	ENST00000518570.2	n.350-11689T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85839 AN: 151988 Hom.: 25207 Cov.: 33

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.565 AC: 85888 AN: 152106 Hom.: 25218 Cov.: 33 AF XY: 0.550 AC XY: 40911 AN XY: 74346

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.544

Alfa AF: 0.601 Hom.: 35058

Bravo AF: 0.562

Asia WGS AF: 0.302 AC: 1052 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756939; hg19: chr6-119340881;