rs6108038

Variant names:

• chr20-839019-G-A
• rs6108038
• NM_001042353.3:c.-98+5068G>A

Variant summary

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

The NM_001042353.3(FAM110A):​c.-98+5068G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0867 in 152,100 control chromosomes in the GnomAD database, including 638 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 0.087 (638 hom., cov: 31)
• Consequence: FAM110A NM_001042353.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM110A	NM_001042353.3	c.-98+5068G>A		intron_variant	Intron 1 of 1	ENST00000381941.8	NP_001035812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM110A	ENST00000381941.8	c.-98+5068G>A		intron_variant	Intron 1 of 1	1	NM_001042353.3	ENSP00000371367.3
FAM110A	ENST00000246100.3	c.-98+2905G>A		intron_variant	Intron 1 of 1	1		ENSP00000246100.3
FAM110A	ENST00000304189.6	c.-206-436G>A		intron_variant	Intron 1 of 2	2		ENSP00000354163.2
FAM110A	ENST00000381939.1	c.-95+5068G>A		intron_variant	Intron 1 of 1	3		ENSP00000371365.1

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13188 AN: 151982 Hom.: 636 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.0820

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

GnomAD4 genome AF: 0.0867 AC: 13194 AN: 152100 Hom.: 638 Cov.: 31 AF XY: 0.0850 AC XY: 6321 AN XY: 74362

African (AFR) AF: 0.122 AC: 5074 AN: 41454

American (AMR) AF: 0.0690 AC: 1054 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3472

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5184

South Asian (SAS) AF: 0.0428 AC: 206 AN: 4812

European-Finnish (FIN) AF: 0.0621 AC: 657 AN: 10586

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0828 AC: 5632 AN: 67996

Other (OTH) AF: 0.0816 AC: 172 AN: 2108

Alfa AF: 0.0834 Hom.: 1060

Bravo AF: 0.0881

Asia WGS AF: 0.0810 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.2
DANN	Benign	0.78
PhyloP100		-0.14
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: rs6108038; hg19: chr20-819662;