rs2282051

Positions:

• chr20-845870-C-G

Variant summary

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

The NM_001042353.3(FAM110A):​c.*178C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 1,369,082 control chromosomes in the GnomAD database, including 11,122 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 0.14 (1527 hom., cov: 32)
  • Exomes 𝑓: 0.12 (9595 hom.)
• Consequence: FAM110A NM_001042353.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

Genes affected

FAM110A (HGNC:16188): (family with sequence similarity 110 member A) Predicted to be located in cytoplasm; microtubule organizing center; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM110A	NM_001042353.3	c.*178C>G		3_prime_UTR_variant	2/2	ENST00000381941.8	NP_001035812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM110A	ENST00000381941.8	c.*178C>G		3_prime_UTR_variant	2/2	1	NM_001042353.3	ENSP00000371367	P1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20574 AN: 152086 Hom.: 1523 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.132

GnomAD4 exome AF: 0.122 AC: 148817 AN: 1216878 Hom.: 9595 Cov.: 18 AF XY: 0.122 AC XY: 72728 AN XY: 593782

Gnomad4 AFR exome AF: 0.177

Gnomad4 AMR exome AF: 0.0858

Gnomad4 ASJ exome AF: 0.162

Gnomad4 EAS exome AF: 0.180

Gnomad4 SAS exome AF: 0.135

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.138

GnomAD4 genome AF: 0.135 AC: 20592 AN: 152204 Hom.: 1527 Cov.: 32 AF XY: 0.135 AC XY: 10038 AN XY: 74428

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0960

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.132

Alfa AF: 0.125 Hom.: 168

Bravo AF: 0.136

Asia WGS AF: 0.146 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.49

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: rs2282051; hg19: chr20-826513; COSMIC: COSV55727032;