rs35031884

chr12-50383790-C-A

Variant summary

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

The NM_001145475.3(FAM186A):c.192+12503G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,738 control chromosomes in the GnomAD database, including 1,350 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 0.11 (1350 hom., cov: 31)
• Consequence: FAM186A NM_001145475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.832

Genes affected

FAM186A (HGNC:26980): (family with sequence similarity 186 member A)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM186A	NM_001145475.3	c.192+12503G>T		intron_variant		ENST00000327337.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM186A	ENST00000327337.6	c.192+12503G>T		intron_variant		5	NM_001145475.3	A2
FAM186A	ENST00000543111.5	c.192+12503G>T		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17429 AN: 151618 Hom.: 1350 Cov.: 31

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.115 AC: 17422 AN: 151738 Hom.: 1350 Cov.: 31 AF XY: 0.112 AC XY: 8269 AN XY: 74136

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.119

Alfa AF: 0.136 Hom.: 190

Bravo AF: 0.106

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	3.3
Dann	Benign	0.61

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: rs35031884; hg19: chr12-50777573;