6-119074043-T-C

Position:

• chr6-119074043-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.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

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 (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM184A	NM_024581.6	c.159+4098A>G		intron_variant		ENST00000338891.12	NP_078857.5
FAM184A	NM_001100411.3	c.-201-49230A>G		intron_variant			NP_001093881.1
FAM184A	NM_001288576.2	c.-201-49230A>G		intron_variant			NP_001275505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM184A	ENST00000338891.12	c.159+4098A>G		intron_variant		1	NM_024581.6	ENSP00000342604	P1
	ENST00000518570.2	n.456+42532T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00684

Gnomad4 FIN AF: 0.0457

Gnomad4 NFE AF: 0.0216

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0601 Hom.: 73

Bravo AF: 0.0674

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs1334927; hg19: chr6-119395208;