chr6-119000386-T-C

Variant names:

• chr6-119000386-T-C
• rs10499090
• NM_024581.6:c.2088+2513A>G

Variant summary

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

The NM_024581.6(FAM184A):​c.2088+2513A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,004 control chromosomes in the GnomAD database, including 11,497 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 0.37 (11497 hom., cov: 31)
• Consequence: FAM184A NM_024581.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM184A	NM_024581.6	c.2088+2513A>G		intron_variant	Intron 9 of 17	ENST00000338891.12	NP_078857.5
FAM184A	NM_001100411.3	c.1728+2513A>G		intron_variant	Intron 9 of 16		NP_001093881.1
FAM184A	NM_001288576.2	c.1728+2513A>G		intron_variant	Intron 9 of 15		NP_001275505.1
LOC124901389	XR_007059729.1	n.77-31019T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM184A	ENST00000338891.12	c.2088+2513A>G		intron_variant	Intron 9 of 17	1	NM_024581.6	ENSP00000342604.7

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56420 AN: 151886 Hom.: 11491 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.371 AC: 56460 AN: 152004 Hom.: 11497 Cov.: 31 AF XY: 0.383 AC XY: 28423 AN XY: 74288

African (AFR) AF: 0.232 AC: 9629 AN: 41462

American (AMR) AF: 0.496 AC: 7571 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3468

East Asian (EAS) AF: 0.682 AC: 3516 AN: 5154

South Asian (SAS) AF: 0.461 AC: 2225 AN: 4826

European-Finnish (FIN) AF: 0.498 AC: 5253 AN: 10554

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25688 AN: 67962

Other (OTH) AF: 0.401 AC: 847 AN: 2112

Alfa AF: 0.371 Hom.: 2106

Bravo AF: 0.370

Asia WGS AF: 0.522 AC: 1813 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10499090; hg19: chr6-119321551;