rs35031884

Variant names:

• chr12-50383790-C-A
• rs35031884
• NM_001145475.3:c.192+12503G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM186A	NM_001145475.3	c.192+12503G>T		intron_variant	Intron 1 of 7	ENST00000327337.6	NP_001138947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM186A	ENST00000327337.6	c.192+12503G>T		intron_variant	Intron 1 of 7	5	NM_001145475.3	ENSP00000329995.5
FAM186A	ENST00000543111.5	c.192+12503G>T		intron_variant	Intron 1 of 7	5		ENSP00000441337.1

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

African (AFR) AF: 0.0340 AC: 1409 AN: 41384

American (AMR) AF: 0.0879 AC: 1331 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5162

South Asian (SAS) AF: 0.105 AC: 502 AN: 4802

European-Finnish (FIN) AF: 0.146 AC: 1542 AN: 10532

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11934 AN: 67938

Other (OTH) AF: 0.119 AC: 252 AN: 2110

Alfa AF: 0.129 Hom.: 455

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
PhyloP100		0.83
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: rs35031884; hg19: chr12-50777573;