rs2282051

Variant names:

• chr20-845870-C-G
• rs2282051
• NM_001042353.3:c.*178C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM110A	NM_001042353.3	c.*178C>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000381941.8	NP_001035812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM110A	ENST00000381941.8	c.*178C>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_001042353.3	ENSP00000371367.3

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

African (AFR) AF: 0.177 AC: 4672 AN: 26360

American (AMR) AF: 0.0858 AC: 1639 AN: 19100

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 2946 AN: 18236

East Asian (EAS) AF: 0.180 AC: 6068 AN: 33778

South Asian (SAS) AF: 0.135 AC: 8222 AN: 60680

European-Finnish (FIN) AF: 0.107 AC: 4736 AN: 44408

Middle Eastern (MID) AF: 0.134 AC: 497 AN: 3720

European-Non Finnish (NFE) AF: 0.118 AC: 113023 AN: 959904

Other (OTH) AF: 0.138 AC: 7014 AN: 50692

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

African (AFR) AF: 0.173 AC: 7203 AN: 41526

American (AMR) AF: 0.0960 AC: 1468 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1070 AN: 5170

South Asian (SAS) AF: 0.146 AC: 703 AN: 4828

European-Finnish (FIN) AF: 0.111 AC: 1175 AN: 10614

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7962 AN: 67994

Other (OTH) AF: 0.132 AC: 278 AN: 2110

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
PhyloP100		0.41
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: rs2282051; hg19: chr20-826513; COSMIC: COSV55727032;